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Eckstein J, Renner A, Zittermann A, Fink T, Sohns C, Niehaus K, Bednarz H, Neumann JM, Piran M, Kellner U, Gummert J. Impact of left atrial appendage fibrosis on atrial fibrillation in patients following coronary bypass surgery. Clin Cardiol 2022; 45:1029-1035. [PMID: 35864729 PMCID: PMC9574744 DOI: 10.1002/clc.23884] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/25/2022] [Accepted: 06/30/2022] [Indexed: 11/09/2022] Open
Abstract
Objectives We aimed to assess the relationship of left atrial appendage (LAA) fibrosis with atrial fibrillation (AF) and postoperative events in patients receiving coronary artery bypass graft surgery (CABG). Background Increased atrial fibrosis has been associated with AF and worse outcome following catheter ablation. Only limited data exists focusing on the impact of LAA fibrosis on AF after CABG. Methods LAA tissue from 164 CABG‐patients was stained with Masson‐Goldner trichrome. The histological landscape was scanned and segmented into superpixels for software analysis (QuPath). A classification algorithm was extensively trained to detect fibrotic superpixels for quantification. In 43 propensity score matched pairs with AF or sinus rhythm (SR), LAA fibrosis was compared. Moreover, subgroups of mitral valve regurgitation (MR) were analyzed as follows: SR, SR + MR, AF and AF + MR. The predictive value of LAA fibrosis postoperative stroke, postoperative AF and mortality was assessed. Results Fibrotic remodeling (%) showed no significant difference for the total cohort between the SR and AF group (SR: 30.8 ± 11.4% and AF: 33.8 ± 16.0%, respectively, p = .32). However, significant fibrotic remodeling was observed for SR and AF subgroups (SR: 27.2 ± 12.2% vs. AF: 35.3 ± 13.7%; respectively, p = .049) and between SR and SR + MR subgroups (SR: 27.2 ± 12.2% vs. SR + MR: 34.9 ± 9.1%, respectively, p = .027). LAA fibrosis was not significantly associated with postoperative stroke, postoperative AF or overall mortality (all p > .05). Conclusion LAA fibrosis may contribute to an individual arrhythmia substrate for AF in patients with AF but also in those with SR and coincidence of MR. LAA fibrosis was not found to be predictive for clinical events in patients after CABG.
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Affiliation(s)
- Jan Eckstein
- Department for Radiology, Nuclear Medicine and Molecular Imaging, Herz- und Diabeteszentrum Nordrhein-Westfalen, Ruhr-Universität Bochum, Bad Oeynhausen, Germany
| | - André Renner
- Clinic for Cardiovascular and Thoracic Surgery, Herz- und Diabeteszentrum Nordrhein-Westfalen, Ruhr-University Bochum, Bad Oeynhausen, Germany
| | - Armin Zittermann
- Clinic for Cardiovascular and Thoracic Surgery, Herz- und Diabeteszentrum Nordrhein-Westfalen, Ruhr-University Bochum, Bad Oeynhausen, Germany
| | - Thomas Fink
- Clinic for Electrophysiology, Herz- und Diabeteszentrum Nordrhein-Westfalen, Ruhr-University Bochum, Bad Oeynhausen, Germany
| | - Christian Sohns
- Clinic for Electrophysiology, Herz- und Diabeteszentrum Nordrhein-Westfalen, Ruhr-University Bochum, Bad Oeynhausen, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, NRW, Bielefeld, Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, NRW, Bielefeld, Germany.,Medical School OWL, AG1: Sustainable Environmental Health Sciences, Bielefeld University, NRW, Bielefeld, Germany
| | - Judith Martha Neumann
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, NRW, Bielefeld, Germany
| | - Misagh Piran
- Department for Radiology, Nuclear Medicine and Molecular Imaging, Herz- und Diabeteszentrum Nordrhein-Westfalen, Ruhr-Universität Bochum, Bad Oeynhausen, Germany
| | - Udo Kellner
- Institute for Pathology and Molecular Pathology, Johannes Wesling Klinikum, Ruhr-University Bochum, Minden, Germany
| | - Jan Gummert
- Clinic for Cardiovascular and Thoracic Surgery, Herz- und Diabeteszentrum Nordrhein-Westfalen, Ruhr-University Bochum, Bad Oeynhausen, Germany
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2
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Zurowietz A, Lehr PP, Kleb M, Merkt N, Gödde V, Bednarz H, Niehaus K, Zörb C. Training grapevines generates a metabolomic signature of wine. Food Chem 2022; 368:130665. [PMID: 34438180 DOI: 10.1016/j.foodchem.2021.130665] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 11/04/2022]
Abstract
Training systems are an option to handle the pronounced apical dominance of grapevines and to influence diverse traits of the corresponding wine. However, it is still unclear if different training systems generate signatures in the metabolome of the wine. By an untargeted metabolomics approach using (SPME) GC-MS wine (volatiles) and leaves were evaluated. Different training directions such as vertical shoot positioning systems, hanging shoot systems, and minimal pruning systems were distinguishable in wine. It was shown, that different training systems generate a metabolomic signature in the wine which was more pronounced than in leaves. Moreover, the sensory analysis showed some changes in the aroma of the different training systems. Thus, the influence of the training system ranges from the leaf metabolome to the wine metabolome.
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Affiliation(s)
- A Zurowietz
- Bielefeld University, Center for Biotechnology & Faculty of Biology, Department of Proteome and Metabolome Research, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Patrick P Lehr
- University of Hohenheim Institute of Crop Science Quality of Plant Products and Viticulture (340e) Schloss Westflügel, 70593 Stuttgart, Germany
| | - M Kleb
- University of Hohenheim Institute of Crop Science Quality of Plant Products and Viticulture (340e) Schloss Westflügel, 70593 Stuttgart, Germany
| | - N Merkt
- University of Hohenheim Institute of Crop Science Quality of Plant Products and Viticulture (340e) Schloss Westflügel, 70593 Stuttgart, Germany
| | - V Gödde
- Bielefeld University, Center for Biotechnology & Faculty of Biology, Department of Proteome and Metabolome Research, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - H Bednarz
- Bielefeld University, Center for Biotechnology & Faculty of Biology, Department of Proteome and Metabolome Research, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - K Niehaus
- Bielefeld University, Center for Biotechnology & Faculty of Biology, Department of Proteome and Metabolome Research, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - C Zörb
- University of Hohenheim Institute of Crop Science Quality of Plant Products and Viticulture (340e) Schloss Westflügel, 70593 Stuttgart, Germany.
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3
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Behr JH, Bednarz H, Gödde V, Niehaus K, Zörb C. Metabolic responses of sugar beet to the combined effect of root hypoxia and NaCl-salinity. J Plant Physiol 2021; 267:153545. [PMID: 34736005 DOI: 10.1016/j.jplph.2021.153545] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/17/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
The combined occurrence of salt stress and hypoxia leads to increased growth reduction and severe toxic effects compared to salt stress alone. In the present work, we analyzed the metabolic response of sugar beet (Beta vulgaris L.) to salt stress combined with hypoxia in roots as well as in young and mature leaves. B. vulgaris plants were grown in a hydroponic culture under low and high salt concentrations combined with normoxic and hypoxic conditions. A non-targeted metabolic approach was used to identify the biochemical pathways underlying the metabolic and physiological adaptation mechanisms. Young and mature leaves showed a similar metabolic response to salt stress alone and combined stresses, accumulating sugar compounds. Osmoprotectants such as proline and pinitol were accumulated under combined stress. Roots exposed to hypoxic conditions showed increased TCA (tricarboxylic acid cycle) intermediates levels such as succinate, fumarate and malate. During hypoxia, the concentration of free amino acids as well as intermediates of the GABA (gamma-aminobutyric acid) shunt increased in roots as well as in leaves. The combination of salt stress and hypoxia results in a severe stress response in roots and leaves. A partial flux of the TCA cycle linked with the GABA shunt might be activated during hypoxia to regain reduction equivalents.
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Affiliation(s)
- Jan Helge Behr
- University of Hohenheim, Institute of Crop Science, Quality of Plant Products; Emil-Wolff-Str. 25, 70599, Stuttgart, Germany; Leibniz Institute of Vegetable and Ornamental Crops, Plant-Microbe Systems, 14979, Grossbeeren, Germany
| | - Hanna Bednarz
- CeBiTec, Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Victoria Gödde
- CeBiTec, Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Karsten Niehaus
- CeBiTec, Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Christian Zörb
- University of Hohenheim, Institute of Crop Science, Quality of Plant Products; Emil-Wolff-Str. 25, 70599, Stuttgart, Germany.
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Neumann JM, Freitag H, Hartmann JS, Niehaus K, Galanis M, Griesshammer M, Kellner U, Bednarz H. Subtyping non-small cell lung cancer by histology-guided spatial metabolomics. J Cancer Res Clin Oncol 2021; 148:351-360. [PMID: 34839410 PMCID: PMC8800912 DOI: 10.1007/s00432-021-03834-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 08/20/2021] [Accepted: 10/11/2021] [Indexed: 01/04/2023]
Abstract
Purpose Most cancer-related deaths worldwide are associated with lung cancer. Subtyping of non-small cell lung cancer (NSCLC) into adenocarcinoma (AC) and squamous cell carcinoma (SqCC) is of importance, as therapy regimes differ. However, conventional staining and immunohistochemistry have their limitations. Therefore, a spatial metabolomics approach was aimed to detect differences between subtypes and to discriminate tumor and stroma regions in tissues. Methods Fresh-frozen NSCLC tissues (n = 35) were analyzed by matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) of small molecules (< m/z 1000). Measured samples were subsequently stained and histopathologically examined. A differentiation of subtypes and a discrimination of tumor and stroma regions was performed by receiver operating characteristic analysis and machine learning algorithms. Results Histology-guided spatial metabolomics revealed differences between AC and SqCC and between NSCLC tumor and tumor microenvironment. A diagnostic ability of 0.95 was achieved for the discrimination of AC and SqCC. Metabolomic contrast to the tumor microenvironment was revealed with an area under the curve of 0.96 due to differences in phospholipid profile. Furthermore, the detection of NSCLC with rarely arising mutations of the isocitrate dehydrogenase (IDH) gene was demonstrated through 45 times enhanced oncometabolite levels. Conclusion MALDI-MSI of small molecules can contribute to NSCLC subtyping. Measurements can be performed intraoperatively on a single tissue section to support currently available approaches. Moreover, the technique can be beneficial in screening of IDH-mutants for the characterization of these seldom cases promoting the development of treatment strategies. Supplementary Information The online version contains supplementary material available at 10.1007/s00432-021-03834-w.
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Affiliation(s)
- Judith Martha Neumann
- Faculty of Biology, Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Hinrich Freitag
- Institut für Pathologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Jasmin Saskia Hartmann
- Faculty of Biology, Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Faculty of Biology, Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Michail Galanis
- Universitätsklinik für Allgemeinchirurgie, Viszeral-, Thorax- und Endokrine Chirurgie, Johannes Wesling Klinikum Minden, Minden, Germany.,Clinic for Thoracic Surgery and Thoracic Endoscopy, University Hospital Bielefeld Mitte, Bielefeld, Germany
| | - Martin Griesshammer
- Universitätsklinik für Hämatologie, Onkologie, Hämostaseologie und Palliativmedizin, Universitätszentrum Innere Medizin, Johannes Wesling Klinikum Minden, Minden, Germany
| | - Udo Kellner
- Institut für Pathologie, Medizinische Hochschule Hannover, Hannover, Germany. .,Institut für Pathologie, Johannes Wesling Klinikum, Minden, Germany.
| | - Hanna Bednarz
- Faculty of Biology, Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany. .,Medical School OWL, AG1: Sustainable Environmental Health Sciences, Bielefeld University, Bielefeld, Germany.
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5
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Creutz I, Busche T, Layer F, Bednarz H, Kalinowski J, Niehaus K. Evaluation of virulence potential of methicillin-sensitive and methicillin-resistant Staphylococcus aureus isolates from a German refugee cohort. Travel Med Infect Dis 2021; 45:102204. [PMID: 34785377 DOI: 10.1016/j.tmaid.2021.102204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Received: 03/23/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 11/15/2022]
Abstract
BACKGROUND Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) seem to be highly transmissible, often infect otherwise healthy humans and frequently occur in hospital outbreaks. METHODS Refugees, living in accommodations in Germany were screened for nasal carriage of S. aureus. The isolates were investigated regarding resistance and virulence, phenotypically and by whole genome data analysis. RESULTS 5.6% (9/161) of the refugees are carriers of S. aureus. 2.5% (4/161) are MRSA carriers. Among the refugees, spa-types t021, t084, t304, t991 and t4983 were detected, as well as the new spa-types t18794 and t18795. t304 and t991 are assumed to be local spa-types from the middle east. The isolates are less resistant and marginal biofilm formers. Each isolate has a remarkable set of virulence genes, although genes, encoding for proteins strongly associated with invasive S. aureus infections, like Panton-Valentine leucocidin, were not detected. CONCLUSION The detection of strains from the middle east, supports the assumption that strains co-travel with the refugees and persist despite a transition of the host's living conditions. Whole genome data analysis does not permit to finally evaluate a germ's virulence. Nevertheless, an impression of the virulence potential of the strains, regarding skills in colonization, resistance, immune evasion, and host cell damaging can be pictured.
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Affiliation(s)
- Ines Creutz
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany; FlüGe Graduate School, School of Public Heath, Bielefeld University, Bielefeld, Germany.
| | - Tobias Busche
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany.
| | - Franziska Layer
- Department of Infectious Diseases, Division Nosocomial Pathogens and Antibiotic Resistances, National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Wernigerode, Germany.
| | - Hanna Bednarz
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany.
| | - Karsten Niehaus
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
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6
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Neumann JM, Niehaus K, Neumann N, Knobloch HC, Bremmer F, Krafft U, Kellner U, Nyirády P, Szarvas T, Bednarz H, Reis H. A new technological approach in diagnostic pathology: mass spectrometry imaging-based metabolomics for biomarker detection in urachal cancer. J Transl Med 2021; 101:1281-1288. [PMID: 34021261 PMCID: PMC8367814 DOI: 10.1038/s41374-021-00612-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 03/16/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 11/18/2022] Open
Abstract
Urachal adenocarcinomas (UrC) are rare but aggressive. Despite being of profound therapeutic relevance, UrC cannot be differentiated by histomorphology alone from other adenocarcinomas of differential diagnostic importance. As no reliable tissue-based diagnostic biomarkers are available, we aimed to detect such by integrating mass-spectrometry imaging-based metabolomics and digital pathology, thus allowing for a multimodal approach on the basis of spatial information. To achieve this, a cohort of UrC (n = 19) and colorectal adenocarcinomas (CRC, n = 27) as the differential diagnosis of highest therapeutic relevance was created, tissue micro-arrays (TMAs) were constructed, and pathological data was recorded. Hematoxylin and eosin (H&E) stained tissue sections were scanned and annotated, enabling an automized discrimination of tumor and non-tumor areas after training of an adequate algorithm. Spectral information within tumor regions, obtained via matrix-assisted laser desorption/ionization (MALDI)-Orbitrap-mass spectrometry imaging (MSI), were subsequently extracted in an automated workflow. On this basis, metabolic differences between UrC and CRC were revealed using machine learning algorithms. As a result, the study demonstrated the feasibility of MALDI-MSI for the evaluation of FFPE tissue in UrC and CRC with the potential to combine spatial metabolomics data with annotated histopathological data from digitalized H&E slides. The detected Area under the curve (AUC) of 0.94 in general and 0.77 for the analyte taurine alone (diagnostic accuracy for taurine: 74%) makes the technology a promising tool in this differential diagnostic dilemma situation. Although the data has to be considered as a proof-of-concept study, it presents a new adoption of this technology that has not been used in this scenario in which reliable diagnostic biomarkers (such as immunohistochemical markers) are currently not available.
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Affiliation(s)
- Judith Martha Neumann
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Nils Neumann
- Research Institute for Cognition and Robotics (CoR-Lab), Bielefeld University, Bielefeld, Germany
| | - Hans Christoph Knobloch
- Department of Urology, University Medical Center Göttingen, University of Göttingen, Göttingen, Germany
| | - Felix Bremmer
- Institute of Pathology, University Medical Center Göttingen, University of Göttingen, Göttingen, Germany
| | - Ulrich Krafft
- Department of Urology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Udo Kellner
- Institut für Pathologie, Johannes Wesling Klinikum Minden, Minden, Germany
| | - Peter Nyirády
- Department of Urology, Semmelweis University Budapest, Budapest, Hungary
| | - Tibor Szarvas
- Department of Urology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Department of Urology, Semmelweis University Budapest, Budapest, Hungary
| | - Hanna Bednarz
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany.
- Medical School OWL, Bielefeld University, Bielefeld, Germany.
| | - Henning Reis
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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Hrbáčková M, Luptovčiak I, Hlaváčková K, Dvořák P, Tichá M, Šamajová O, Novák D, Bednarz H, Niehaus K, Ovečka M, Šamaj J. Overexpression of alfalfa SIMK promotes root hair growth, nodule clustering and shoot biomass production. Plant Biotechnol J 2021; 19:767-784. [PMID: 33112469 PMCID: PMC8051612 DOI: 10.1111/pbi.13503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/30/2020] [Revised: 10/08/2020] [Accepted: 10/15/2020] [Indexed: 05/03/2023]
Abstract
Nitrogen-fixing rhizobia and legumes have developed complex mutualistic mechanism that allows to convert atmospheric nitrogen into ammonia. Signalling by mitogen-activated protein kinases (MAPKs) seems to be involved in this symbiotic interaction. Previously, we reported that stress-induced MAPK (SIMK) shows predominantly nuclear localization in alfalfa root epidermal cells. Nevertheless, SIMK is activated and relocalized to the tips of growing root hairs during their development. SIMK kinase (SIMKK) is a well-known upstream activator of SIMK. Here, we characterized production parameters of transgenic alfalfa plants with genetically manipulated SIMK after infection with Sinorhizobium meliloti. SIMKK RNAi lines, causing strong downregulation of both SIMKK and SIMK, showed reduced root hair growth and lower capacity to form infection threads and nodules. In contrast, constitutive overexpression of GFP-tagged SIMK promoted root hair growth as well as infection thread and nodule clustering. Moreover, SIMKK and SIMK downregulation led to decrease, while overexpression of GFP-tagged SIMK led to increase of biomass in above-ground part of plants. These data suggest that genetic manipulations causing downregulation or overexpression of SIMK affect root hair, nodule and shoot formation patterns in alfalfa, and point to the new biotechnological potential of this MAPK.
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Affiliation(s)
- Miroslava Hrbáčková
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Ivan Luptovčiak
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Kateřina Hlaváčková
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Petr Dvořák
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Michaela Tichá
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Olga Šamajová
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Dominik Novák
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Hanna Bednarz
- Faculty of BiologyCenter for Biotechnology – CeBiTecUniversität BielefeldBielefeldGermany
| | - Karsten Niehaus
- Faculty of BiologyCenter for Biotechnology – CeBiTecUniversität BielefeldBielefeldGermany
| | - Miroslav Ovečka
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Jozef Šamaj
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
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8
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Albicoro FJ, Draghi WO, Martini MC, Salas ME, Torres Tejerizo GA, Lozano MJ, López JL, Vacca C, Cafiero JH, Pistorio M, Bednarz H, Meier D, Lagares A, Niehaus K, Becker A, Del Papa MF. The two-component system ActJK is involved in acid stress tolerance and symbiosis in Sinorhizobium meliloti. J Biotechnol 2021; 329:80-91. [PMID: 33539896 DOI: 10.1016/j.jbiotec.2021.01.006] [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: 11/27/2020] [Revised: 12/31/2020] [Accepted: 01/08/2021] [Indexed: 01/25/2023]
Abstract
The nitrogen-fixing α-proteobacterium Sinorhizobium meliloti genome codifies at least 50 response regulator (RR) proteins mediating different and, in many cases, unknown processes. RR-mutant library screening allowed us to identify genes potentially implicated in survival to acid conditions. actJ mutation resulted in a strain with reduced growth rate under mildly acidic conditions as well as a lower capacity to tolerate a sudden shift to lethal acidic conditions compared with the parental strain. Mutation of the downstream gene actK, which encodes for a histidine kinase, showed a similar phenotype in acidic environments suggesting a functional two-component system. Interestingly, even though nodulation kinetics, quantity, and macroscopic morphology of Medicago sativa nodules were not affected in actJ and actK mutants, ActK was required to express the wild-type nitrogen fixation phenotype and ActJK was necessary for full bacteroid development and nodule occupancy. The actJK regulatory system presented here provides insights into an evolutionary process in rhizobium adaptation to acidic environments and suggests that actJK-controlled functions are crucial for optimal symbiosis development.
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Affiliation(s)
- Francisco J Albicoro
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Walter O Draghi
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María C Martini
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María E Salas
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - G A Torres Tejerizo
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mauricio J Lozano
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - José L López
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Carolina Vacca
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Juan H Cafiero
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mariano Pistorio
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Hanna Bednarz
- CeBiTec, Centrum für Biotechnologie, Universität Bielefeld, Bielefeld, Germany
| | - Doreen Meier
- CeBiTec, Centrum für Biotechnologie, Universität Bielefeld, Bielefeld, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Antonio Lagares
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Karsten Niehaus
- CeBiTec, Centrum für Biotechnologie, Universität Bielefeld, Bielefeld, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany; Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - M F Del Papa
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.
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9
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Neumann JM, Niehaus K, Neumann N, Knobloch HC, Bremmer F, Krafft U, Kellner U, Nyirády P, Szarvas T, Bednarz H, Reis H. Correction to: A new technological approach in diagnostic pathology: mass spectrometry imaging-based metabolomics for biomarker detection in urachal cancer. J Transl Med 2021; 101:1414. [PMID: 36775441 PMCID: PMC8440205 DOI: 10.1038/s41374-021-00625-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Judith Martha Neumann
- grid.7491.b0000 0001 0944 9128Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- grid.7491.b0000 0001 0944 9128Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Nils Neumann
- grid.7491.b0000 0001 0944 9128Research Institute for Cognition and Robotics (CoR-Lab), Bielefeld University, Bielefeld, Germany
| | - Hans Christoph Knobloch
- grid.411984.10000 0001 0482 5331Department of Urology, University Medical Center Göttingen, University of Göttingen, Göttingen, Germany
| | - Felix Bremmer
- grid.411984.10000 0001 0482 5331Institute of Pathology, University Medical Center Göttingen, University of Göttingen, Göttingen, Germany
| | - Ulrich Krafft
- grid.410718.b0000 0001 0262 7331Department of Urology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Udo Kellner
- grid.477456.3Institut für Pathologie, Johannes Wesling Klinikum Minden, Minden, Germany
| | - Peter Nyirády
- grid.11804.3c0000 0001 0942 9821Department of Urology, Semmelweis University Budapest, Budapest, Hungary
| | - Tibor Szarvas
- grid.410718.b0000 0001 0262 7331Department of Urology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany ,grid.11804.3c0000 0001 0942 9821Department of Urology, Semmelweis University Budapest, Budapest, Hungary
| | - Hanna Bednarz
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany. .,Medical School OWL, Bielefeld University, Bielefeld, Germany.
| | - Henning Reis
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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10
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Lebrazi S, Niehaus K, Bednarz H, Fadil M, Chraibi M, Fikri-Benbrahim K. Screening and optimization of indole-3-acetic acid production and phosphate solubilization by rhizobacterial strains isolated from Acacia cyanophylla root nodules and their effects on its plant growth. J Genet Eng Biotechnol 2020; 18:71. [PMID: 33175273 PMCID: PMC7658270 DOI: 10.1186/s43141-020-00090-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 02/12/2020] [Accepted: 11/02/2020] [Indexed: 11/18/2022]
Abstract
Background Plant growth-promoting rhizobacteria (PGPR) are known to improve plant growth and are used as biofertilizers, thanks to their numerous benefits to agriculture such as phosphorus solubilization and phytohormone production. In this paper, four rhizospheric bacteria (Phyllobacterium sp., Bacillus sp., Agrobacterium sp., and Rhizobium sp.) isolated from surface-sterilized root nodules of Acacia cyanophylla were tested for their ability to solubilize inorganic phosphate and to produce indole-3-acetic acid (IAA) under laboratory conditions. Then, the best IAA producer (Rhizobium sp.) was selected to test optimized conditions for IAA production. Finally, the effect of the four strains on plant growth for A. cyanophylla was evaluated in vivo. Results The results showed that the totality of the tested isolates had solubilized inorganic phosphate (P) in both NBRIP (National Botanical Research Institute Phosphate) and PVK (Pikovskaya) media. Bacillus sp. was a high P-solubilizer and showed maximum solubilization in PVK (519 μg ml-1) and NBRIP (782 μg ml-1). The optimization of maximum phosphate solubilization was done using different sources of carbon (1%) and nitrogen (0.1%). Glucose and ammonium sulfate were selected to be the best carbon and nitrogen source for phosphate solubilization by all tested strains, except for Phyllobacterium sp., which recorded the highest phosphate solubilization with ammonium nitrate. The IAA production by the tested strains indicated that Rhizobium sp. produced the highest amount of IAA (90.21 μg ml-1) in culture media supplemented with L-tryptophan. The best production was observed with L-Trp concentration of 0.2% (116.42 μg ml-1) and at an initial pH of 9 (116.07 μg ml-1). The effect of NaCl on IAA production was tested at concentrations of 0 to 5% and the maximum production of 89.43 μg ml-1 was found at 2% NaCl. The extraction of crude IAA from this strain was done and purity was confirmed with Thin Layer Chromatography (TLC) analysis. A specific spot from the extracted IAA production was found to correspond with a standard spot of IAA with the same Rf value. Finally, the tested PGPR demonstrated growth stimulatory effects on Acacia cyanophylla seedlings in vivo, with a great increase of shoots’ and roots’ dry weights, and shoot length compared to control. The rhizobacterial isolates were identified by 16S rDNA sequence analysis as Agrobacterium sp. NA11001, Phyllobacterium sp. C65, Bacillus sp. CS14, and Rhizobium sp. V3E1. Conclusion This study highlights the importance of the use of phosphate solubilizing and IAA producer microorganisms as biofertilizers to increase crop yields. The studied strains showed a significant phosphate solubilization potential and IAA production. The use of selected strains as inoculants would be interesting, in particular with a view of promoting sustainable agriculture. However, further studies to verify the efficacy of the best isolates in situ is certainly required.
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Affiliation(s)
- Sara Lebrazi
- Laboratory of Microbial Biotechnology, Faculty of Sciences and Technology, Sidi Mohamed Ben Abdellah University, P.O. Box 2202, Fez, Morocco.
| | - Karsten Niehaus
- Proteome and Metabolome Research, Faculty of Biology Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Faculty of Biology Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Mouhcine Fadil
- Physico-Chemical Laboratory of Inorganic and Organic Materials, Materials Science Center (MSC), Ecole Normale Supérieure, Mohammed V University in Rabat, Rabat, Morocco
| | - Marwa Chraibi
- Laboratory of Microbial Biotechnology, Faculty of Sciences and Technology, Sidi Mohamed Ben Abdellah University, P.O. Box 2202, Fez, Morocco
| | - Kawtar Fikri-Benbrahim
- Laboratory of Microbial Biotechnology, Faculty of Sciences and Technology, Sidi Mohamed Ben Abdellah University, P.O. Box 2202, Fez, Morocco
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11
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Sahin M, Neumann JM, Riefke B, Bednarz H, Gutberlet K, Giampà M, Niehaus K, Fatangare A. Spatial evaluation of long-term metabolic changes induced by cisplatin nephrotoxicity. Toxicol Lett 2020; 334:36-43. [PMID: 32941993 DOI: 10.1016/j.toxlet.2020.09.006] [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: 06/17/2020] [Revised: 09/07/2020] [Accepted: 09/10/2020] [Indexed: 10/23/2022]
Abstract
Cisplatin is a widely used chemotherapeutic agent. However, it is causing nephrotoxic side effects including a reduced glomerular filtration rate and acute kidney injury. Although kidneys can recover to an extent from the treatment, long-term damage is possible. While a lot of research is focusing on short-term effects, little is known about adverse metabolic effects in the process of recovery. In this study, male Han Wistar rats were dosed with a single intraperitoneal injection of 3 mg/kg cisplatin. Urine and kidney samples were harvested 3, 8 and 26 days after administration. Tubular injury was demonstrated through urinary biomarkers. Complementing this, mass spectrometry imaging gives insight on molecular alterations on a spatial level, thus making it well suited to analyze short- and long-term disturbances. Various metabolic pathways seem to be affected, as changes in a wide range of metabolites were observed between treated and control animals. Besides previously reported early changes in kidney metabolism, unprecedented long-term effects were detected including deviation in nucleotides, antioxidants, and phospholipids.
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Affiliation(s)
- Mikail Sahin
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Judith M Neumann
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Bjoern Riefke
- Toxicology, Translational Science, Pharmaceuticals Division, Bayer AG, Berlin, Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Katrin Gutberlet
- Toxicology, Translational Science, Pharmaceuticals Division, Bayer AG, Berlin, Germany
| | - Marco Giampà
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Amol Fatangare
- Toxicology, Translational Science, Pharmaceuticals Division, Bayer AG, Berlin, Germany.
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12
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Kampa JM, Kellner U, Marsching C, Ramallo Guevara C, Knappe UJ, Sahin M, Giampà M, Niehaus K, Bednarz H. Glioblastoma multiforme: Metabolic differences to peritumoral tissue and
IDH
‐mutated gliomas revealed by mass spectrometry imaging. Neuropathology 2020; 40:546-558. [DOI: 10.1111/neup.12671] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/20/2020] [Accepted: 03/22/2020] [Indexed: 01/19/2023]
Affiliation(s)
- Judith M. Kampa
- Proteome and Metabolome Research, Faculty of Biology & Center for Biotechnology Bielefeld University Bielefeld Germany
| | - Udo Kellner
- Institut für Pathologie, Johannes Wesling Klinikum Minden Germany
| | - Christian Marsching
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS) Mannheim University of Applied Sciences Mannheim Germany
| | - Carina Ramallo Guevara
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS) Mannheim University of Applied Sciences Mannheim Germany
| | - Ulrich J. Knappe
- Klinik für Neurochirurgie, Johannes Wesling Klinikum Minden Germany
| | - Mikail Sahin
- Proteome and Metabolome Research, Faculty of Biology & Center for Biotechnology Bielefeld University Bielefeld Germany
| | - Marco Giampà
- Proteome and Metabolome Research, Faculty of Biology & Center for Biotechnology Bielefeld University Bielefeld Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Faculty of Biology & Center for Biotechnology Bielefeld University Bielefeld Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Faculty of Biology & Center for Biotechnology Bielefeld University Bielefeld Germany
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13
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Kamjijam B, Bednarz H, Suwannaporn P, Jom KN, Niehaus K. Localization of amino acids in germinated rice grain: Gamma-aminobutyric acid and essential amino acids production approach. J Cereal Sci 2020. [DOI: 10.1016/j.jcs.2020.102958] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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14
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Schäfermann J, Kliewer G, Lösch J, Bednarz H, Giampà M, Niehaus K. Immersion by rotation-based application of the matrix for fast and reproducible sample preparations and robust results in mass spectrometry imaging. J Mass Spectrom 2020; 55:e4488. [PMID: 31826308 DOI: 10.1002/jms.4488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/17/2019] [Revised: 11/22/2019] [Accepted: 12/08/2019] [Indexed: 06/10/2023]
Abstract
Automated matrix deposition for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is crucial for producing reproducible analyte ion signals. Here we report an innovative method employing an automated immersion apparatus, which enables a robust matrix deposition within 5 minutes and with scalable throughput by using MAPS matrix and non-polar solvents. MSI results received from mouse heart and rat brain tissues were qualitatively similar to those from nozzle sprayed samples with respect to peak number and quality of the ion images. Overall, the immersion-method enables a fast and careful matrix deposition and has the future potential for implementation in clinical tissue diagnostics.
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Affiliation(s)
- Johanna Schäfermann
- MSI Diagnostics GmbH, Bielefeld, Germany
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Georg Kliewer
- MSI Diagnostics GmbH, Bielefeld, Germany
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | | | - Hanna Bednarz
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Marco Giampà
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Karsten Niehaus
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany
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15
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Kampa JM, Sahin M, Slopianka M, Giampà M, Bednarz H, Ernst R, Riefke B, Niehaus K, Fatangare A. Mass spectrometry imaging reveals lipid upregulation and bile acid changes indicating amitriptyline induced steatosis in a rat model. Toxicol Lett 2020; 325:43-50. [PMID: 32092452 DOI: 10.1016/j.toxlet.2020.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 09/26/2019] [Revised: 02/03/2020] [Accepted: 02/14/2020] [Indexed: 12/16/2022]
Abstract
As a consequence of the detoxification process, drugs and drug related metabolites can accumulate in the liver, resulting in drug induced liver injury (DILI), which is the major cause for dose limitation. Amitriptyline, a commonly used tricyclic anti-depressant, is known to cause DILI. The mechanism of Amitriptyline induced liver injury is not yet completely understood. However, as it undergoes extensive hepatic metabolism, unraveling the molecular changes in the liver upon Amitriptyline treatment can help understand Amitriptyline's mode of toxicity. In this study, Amitriptyline treated male rat liver tissue was analyzed using Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging (MALDI-MSI) to investigate the spatial abundances of Amitriptyline, lipids, and bile acids. The metabolism of Amitriptyline in liver tissue was successfully demonstrated, as the spatial distribution of Amitriptyline and its metabolites localize throughout treatment group liver samples. Several lipids appear upregulated, from which nine were identified as distinct phosphatidylcholine (PC) species. The detected bile acids were found to be lower in Amitriptyline treatment group. The combined results from histological findings, Oil Red O staining, and lipid zonation by MSI revealed lipid upregulation in the periportal area indicating drug induced macrovesicular steatosis (DIS).
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Affiliation(s)
- Judith M Kampa
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Mikail Sahin
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Markus Slopianka
- Metabolic Profiling and Clinical Pathology, Investigational Toxicology, Pharmaceuticals Division, Bayer AG, Berlin, Germany
| | - Marco Giampà
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Rainer Ernst
- Metabolic Profiling and Clinical Pathology, Investigational Toxicology, Pharmaceuticals Division, Bayer AG, Berlin, Germany
| | - Bjoern Riefke
- Metabolic Profiling and Clinical Pathology, Investigational Toxicology, Pharmaceuticals Division, Bayer AG, Berlin, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Amol Fatangare
- Metabolic Profiling and Clinical Pathology, Investigational Toxicology, Pharmaceuticals Division, Bayer AG, Berlin, Germany.
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16
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Abstract
Alkaloids are common secondary metabolites found also in plants of the large family of Solanaceae, and they contribute frequently to the economic importance of these plants as food, spices, drugs, or pharmaceuticals. Matrix-assisted laser desorption/ionization mass spectrometry imaging was applied to visualize the spatial localization of the main steroidal alkaloids in diverse plant tissues of Lycopersicon esculentum, Solanum nigrum, and Solanum dulcamara. Among others, the basic aglycons, tomatidenol, tomatidine, solasodine, and soladulcine, along with their corresponding glycoalkaloids, were identified with distinct distributions within plant tissue structures and plant parts and with respect to the degree of ripeness. The alkaloids are identified by their mass and fragmentation pattern. Multivariate unsupervised principal compound analysis and the k-means clustering analysis were calculated on the basis of all peaks, automatically picked from all selected regions, with total ion count normalization resulting in characterization of the tissues and organs with respect to their chemical similarity. It can therefore be concluded that the tissue-specific localizations of alkaloids in nightshades depend upon the ripeness status and the developmental stage of the plants.
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Affiliation(s)
- Hanna Bednarz
- Proteome and Metabolome Research, Faculty of Biology & Center for Biotechnology (CeBiTec) , Universität Bielefeld , Universitätsstraße 25 , 33615 Bielefeld , Germany
| | - Nils Roloff
- Proteome and Metabolome Research, Faculty of Biology & Center for Biotechnology (CeBiTec) , Universität Bielefeld , Universitätsstraße 25 , 33615 Bielefeld , Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Faculty of Biology & Center for Biotechnology (CeBiTec) , Universität Bielefeld , Universitätsstraße 25 , 33615 Bielefeld , Germany
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17
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Bednarz H, Kana R. A-24 Metacognition and behavioral regulation associated with distinct connectivity patterns in autism spectrum disorder. Arch Clin Neuropsychol 2019. [DOI: 10.1093/arclin/acz034.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Objective
Executive function (EF) deficits are well documented in children with autism spectrum disorder (ASD)1-2 and are commonly measured clinically using parent ratings3. No studies have investigated whether parent ratings of EF predict brain connectivity in ASD.
Aim
Examine whether the Behavior Rating Inventory of Executive Function (BRIEF) predicts functional brain connectivity in ASD.
Method
Resting-state fMRI and behavioral data were obtained from the Autism Brain Imaging Data Exchange (ABIDE-II) database6 (n = 106 ASD, ages 5-13). ROI-to-ROI (Region of Interest) connectivity was computed for 132 ROIs spanning the whole brain, defined using Conn Toolbox. Multiple regression analyses examined the effect of BRIEF metacognition on connectivity while controlling for BRIEF behavioral regulation, and vice versa. Age, sex, and full-scale IQ were included as covariates. FDR correction was used (p < 0.05).
Results
More severe deficits in metacognition were associated with stronger connectivity between the left hippocampus and several ROIs, including the cerebellum and planum temporale. More severe deficits in metacognition were associated with weaker right hippocampus – right frontal pole connectivity. More severe deficits in behavioral regulation were associated with stronger connectivity between subcortical regions (i.e., thalamus, putamen, and caudate) and regions involved in motor (superior frontal gyrus) and limbic systems (cingulate gyrus). More severe behavioral regulation deficits were associated with weaker cerebellar-cerebellar connectivity.
Conclusions
Findings suggest that parent-ratings of metacognitive abilities in children with ASD are associated with hippocampal connectivity, while behavioral regulation abilities are associated with thalamic and striatum connections. These results build upon previous studies of metacognition and behavioral regulation 5,6.
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18
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Seeger B, Mentz A, Knebel C, Schmidt F, Bednarz H, Niehaus K, Albaum S, Kalinowski J, Noll T, Steinberg P, Marx-Stoelting P, Heise T. Assessment of mixture toxicity of (tri)azoles and their hepatotoxic effects in vitro by means of omics technologies. Arch Toxicol 2019; 93:2321-2333. [PMID: 31254001 DOI: 10.1007/s00204-019-02502-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 04/26/2019] [Accepted: 06/17/2019] [Indexed: 01/08/2023]
Abstract
Consumers are constantly exposed to chemical mixtures such as multiple residues of different pesticides via the diet. This raises questions concerning potential combination effects, especially because these substances are tested for regulatory purposes on an individual basis. With approximately 500 active substances approved as pesticides, there are too many possible combinations to be tested in standard animal experiments generally requested for regulatory purposes. Therefore, the development of in vitro tools and alternative testing strategies for the assessment of mixture effects is extremely important. As a first step in the development of such in vitro tools, we used (tri)azoles as model substances in a set of different cell lines derived from the primary target organ of these substances, the liver (human: HepaRG, rat: H4IIE). Concentrations were reconciled with measured tissue concentrations obtained from in vivo experiments to ensure comparable effect levels. The effects of the substances were subsequently analyzed by transcriptomics and metabolomics techniques and compared to data from corresponding in vivo studies. The results show that similar toxicity pathways are affected by substances and combinations, thus indicating a similar mode of action and additive effects. Two biomarkers obtained by the approach, CAR and Cyp1A1, were used for mixture toxicity modeling and confirmed the concentration-additive effects, thus supporting the selected testing strategy and raising hope for the development of in vitro methods suitable to detect combination effects and prioritize mixtures of concern for further testing.
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Affiliation(s)
- Bettina Seeger
- Institute for Food Toxicology and Center for Alternatives and Complementary Methods to Animal Experiments, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Almut Mentz
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Constanze Knebel
- Department for Pesticide Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Flavia Schmidt
- Department for Pesticide Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Hanna Bednarz
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Stephan Albaum
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Thomas Noll
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Pablo Steinberg
- Institute for Food Toxicology and Center for Alternatives and Complementary Methods to Animal Experiments, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Max Rubner-Institute, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany
| | - Philip Marx-Stoelting
- Department for Pesticide Safety, German Federal Institute for Risk Assessment, Berlin, Germany.
| | - Tanja Heise
- Department for Pesticide Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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19
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Wüllems K, Kölling J, Bednarz H, Niehaus K, Hans VH, Nattkemper TW. Detection and visualization of communities in mass spectrometry imaging data. BMC Bioinformatics 2019; 20:303. [PMID: 31164082 PMCID: PMC6549267 DOI: 10.1186/s12859-019-2890-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 01/28/2019] [Accepted: 05/10/2019] [Indexed: 11/10/2022] Open
Abstract
Background The spatial distribution and colocalization of functionally related metabolites is analysed in order to investigate the spatial (and functional) aspects of molecular networks. We propose to consider community detection for the analysis of m/z-images to group molecules with correlative spatial distribution into communities so they hint at functional networks or pathway activity. To detect communities, we investigate a spectral approach by optimizing the modularity measure. We present an analysis pipeline and an online interactive visualization tool to facilitate explorative analysis of the results. The approach is illustrated with synthetical benchmark data and two real world data sets (barley seed and glioblastoma section). Results For the barley sample data set, our approach is able to reproduce the findings of a previous work that identified groups of molecules with distributions that correlate with anatomical structures of the barley seed. The analysis of glioblastoma section data revealed that some molecular compositions are locally focused, indicating the existence of a meaningful separation in at least two areas. This result is in line with the prior histological knowledge. In addition to confirming prior findings, the resulting graph structures revealed new subcommunities of m/z-images (i.e. metabolites) with more detailed distribution patterns. Another result of our work is the development of an interactive webtool called GRINE (Analysis of GRaph mapped Image Data NEtworks). Conclusions The proposed method was successfully applied to identify molecular communities of laterally co-localized molecules. For both application examples, the detected communities showed inherent substructures that could easily be investigated with the proposed visualization tool. This shows the potential of this approach as a complementary addition to pixel clustering methods. Electronic supplementary material The online version of this article (10.1186/s12859-019-2890-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karsten Wüllems
- International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes", Bielefeld University, Universitätsstraße 25, Bielefeld, 33613, Germany. .,Biodata Mining Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, Bielefeld, 33613, Germany. .,Center for Biotechnology (CeBiTec), Universitätsstraße 25, Bielefeld, 33613, Germany.
| | - Jan Kölling
- International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes", Bielefeld University, Universitätsstraße 25, Bielefeld, 33613, Germany.,Biodata Mining Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, Bielefeld, 33613, Germany
| | - Hanna Bednarz
- Center for Biotechnology (CeBiTec), Universitätsstraße 25, Bielefeld, 33613, Germany.,Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Universitätsstraße 25, Bielefeld, 33613, Germany
| | - Karsten Niehaus
- Center for Biotechnology (CeBiTec), Universitätsstraße 25, Bielefeld, 33613, Germany.,Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Universitätsstraße 25, Bielefeld, 33613, Germany
| | - Volkmar H Hans
- Department of Neuropathology, Institute for Clinical Pathology, Dietrich-Bonhoeffer-Klinikum, Salvador-Allende-Straße 30, Neubrandenburg, 17036, Germany.,Department of Neuropathology, Essen University Hospital (AöR), Hufelandstraße 55, Essen, 45147, Germany
| | - Tim W Nattkemper
- Biodata Mining Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, Bielefeld, 33613, Germany.,Center for Biotechnology (CeBiTec), Universitätsstraße 25, Bielefeld, 33613, Germany
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20
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Verwaaijen B, Wibberg D, Winkler A, Zrenner R, Bednarz H, Niehaus K, Grosch R, Pühler A, Schlüter A. A comprehensive analysis of the Lactuca sativa, L. transcriptome during different stages of the compatible interaction with Rhizoctonia solani. Sci Rep 2019; 9:7221. [PMID: 31076623 PMCID: PMC6510776 DOI: 10.1038/s41598-019-43706-5] [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: 12/12/2018] [Accepted: 04/30/2019] [Indexed: 12/19/2022] Open
Abstract
The leafy green vegetable Lactuca sativa, L. is susceptible to the soil-born fungus Rhizoctonia solani AG1-IB. In a previous study, we reported on the transcriptional response of R. solani AG1-IB (isolate 7/3/14) during the interspecies interaction with L. sativa cv. Tizian by means of RNA sequencing. Here we present the L. sativa transcriptome and metabolome from the same experimental approach. Three distinct interaction zones were sampled and compared to a blank (non-inoculated) sample: symptomless zone 1, zone 2 showing light brown discoloration, and a dark brown zone 3 characterized by necrotic lesions. Throughout the interaction, we observed a massive reprogramming of the L. sativa transcriptome, with 9231 unique genes matching the threshold criteria for differential expression. The lettuce transcriptome of the light brown zone 2 presents the most dissimilar profile compared to the uninoculated zone 4, marking the main stage of interaction. Transcripts putatively encoding several essential proteins that are involved in maintaining jasmonic acid and auxin homeostasis were found to be negatively regulated. These and other indicator transcripts mark a potentially inadequate defence response, leading to a compatible interaction. KEGG pathway mapping and GC-MS metabolome data revealed large changes in amino acid, lignin and hemicellulose related pathways and related metabolites.
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Affiliation(s)
- Bart Verwaaijen
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
- Computational Biology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Anika Winkler
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Rita Zrenner
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Hanna Bednarz
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Rita Grosch
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Alfred Pühler
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
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21
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Bednarz H, Kana R. B - 06The Relationship Between Executive and Social Functioning in Children with Autism Spectrum Disorder. Arch Clin Neuropsychol 2018. [DOI: 10.1093/arclin/acy061.82] [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: 11/12/2022] Open
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Storck J, Homburg S, Feldhans T, Bednarz H, Niehaus K, Patel A. Microencapsulation as a tool to produce multicellular tumor spheroids. CHEM-ING-TECH 2018. [DOI: 10.1002/cite.201855183] [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: 11/11/2022]
Affiliation(s)
- J. L. Storck
- Bielefeld University of Applied Sciences; Fermentation and Formulation of Biologicals and Chemicals; Interaktion 1 33619 Bielefeld Germany
| | - S. V. Homburg
- Bielefeld University of Applied Sciences; Fermentation and Formulation of Biologicals and Chemicals; Interaktion 1 33619 Bielefeld Germany
| | - T. Feldhans
- Bielefeld University of Applied Sciences; Fermentation and Formulation of Biologicals and Chemicals; Interaktion 1 33619 Bielefeld Germany
| | - H. Bednarz
- Bielefeld University; Proteome and Metabolome Research; Universiätsstraße 25 33615 Bielefeld Germany
| | - K. Niehaus
- Bielefeld University; Proteome and Metabolome Research; Universiätsstraße 25 33615 Bielefeld Germany
| | - A. Patel
- Bielefeld University of Applied Sciences; Fermentation and Formulation of Biologicals and Chemicals; Interaktion 1 33619 Bielefeld Germany
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Horatz K, Giampà M, Karpov Y, Sahre K, Bednarz H, Kiriy A, Voit B, Niehaus K, Hadjichristidis N, Michels DL, Lissel F. Conjugated Polymers as a New Class of Dual-Mode Matrices for MALDI Mass Spectrometry and Imaging. J Am Chem Soc 2018; 140:11416-11423. [DOI: 10.1021/jacs.8b06637] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kilian Horatz
- Institute of Macromolecular Chemistry, Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany
- Organic Chemistry of Polymers, Technische Universität Dresden, Mommsenstrasse 4, 01062 Dresden, Germany
| | - Marco Giampà
- Center for Biotechnology and Department for Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Yevhen Karpov
- Institute of Macromolecular Chemistry, Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany
| | - Karin Sahre
- Institute of Macromolecular Chemistry, Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany
| | - Hanna Bednarz
- Center for Biotechnology and Department for Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Anton Kiriy
- Institute of Macromolecular Chemistry, Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany
| | - Brigitte Voit
- Institute of Macromolecular Chemistry, Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany
- Organic Chemistry of Polymers, Technische Universität Dresden, Mommsenstrasse 4, 01062 Dresden, Germany
| | - Karsten Niehaus
- Center for Biotechnology and Department for Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Nikos Hadjichristidis
- Physical Sciences and Engineering Division, KAUST Catalysis Center, Polymer Synthesis Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Dominik L. Michels
- Computer, Electrical and Mathematical Sciences and Engineering Division, KAUST Visual Computing Center, Computational Sciences Group, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Franziska Lissel
- Institute of Macromolecular Chemistry, Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany
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Wagner C, Bonte A, Brühl L, Niehaus K, Bednarz H, Matthäus B. Micro-organisms growing on rapeseed during storage affect the profile of volatile compounds of virgin rapeseed oil. J Sci Food Agric 2018; 98:2147-2155. [PMID: 28960362 DOI: 10.1002/jsfa.8699] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 06/30/2017] [Revised: 09/17/2017] [Accepted: 09/18/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Micro-organisms populate on rapeseed after harvest during storage depending on the growing conditions. The composition of the bacterial colonization is unknown, although its contribution to the profile of volatile aroma-active compounds determines the sensory quality of virgin cold-pressed rapeseed oil. RESULTS From four rapeseed samples, 46 bacterial strains were isolated. By DNA-sequencing, the identification of four bacteria species and 17 bacteria genera was possible. In total, 22 strains were selected, based on their typical off-flavors resembling those of virgin sensory bad cold-pressed rapeseed oils. The cultivation of these strains on rapeseed meal agar and examination of volatile compounds by solid phase microextraction-gas chromatography-mass spectrometry allowed the identification of 29 different compounds, mainly degradation products of fatty acids such as alkanes, alkenes, aldehydes, ketones and alcohols and, in addition, sulfur-containing compounds, including one terpene and three pyrazines. From these compounds, 19 are described as aroma-active in the literature. CONCLUSION Micro-organisms populating on rapeseed during storage may strongly influence the sensory quality of virgin rapeseed oil as a result of the development of volatile aroma-active metabolic products. It can be assumed that occurrence of off-flavor of virgin rapeseed oils on the market are the result of metabolic degradation products produced by micro-organisms populating on rapeseed during storage. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Claudia Wagner
- Institute for Food Chemistry, University of Münster, Münster, Germany
| | - Anja Bonte
- Department of Safety and Quality of Cereals, Federal Research Institute of Nutrition and Food, Max Rubner-Institut, Detmold, Germany
| | - Ludger Brühl
- Department of Safety and Quality of Cereals, Federal Research Institute of Nutrition and Food, Max Rubner-Institut, Detmold, Germany
| | - Karsten Niehaus
- Department of Proteome and Metabolome Research, Faculty of Biology & Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Hanna Bednarz
- Department of Proteome and Metabolome Research, Faculty of Biology & Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Bertrand Matthäus
- Department of Safety and Quality of Cereals, Federal Research Institute of Nutrition and Food, Max Rubner-Institut, Detmold, Germany
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Uddin LQ, Dajani DR, Voorhies W, Bednarz H, Kana RK. Progress and roadblocks in the search for brain-based biomarkers of autism and attention-deficit/hyperactivity disorder. Transl Psychiatry 2017; 7:e1218. [PMID: 28892073 PMCID: PMC5611731 DOI: 10.1038/tp.2017.164] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 06/07/2017] [Indexed: 11/22/2022] Open
Abstract
Children with neurodevelopmental disorders benefit most from early interventions and treatments. The development and validation of brain-based biomarkers to aid in objective diagnosis can facilitate this important clinical aim. The objective of this review is to provide an overview of current progress in the use of neuroimaging to identify brain-based biomarkers for autism spectrum disorder (ASD) and attention-deficit/hyperactivity disorder (ADHD), two prevalent neurodevelopmental disorders. We summarize empirical work that has laid the foundation for using neuroimaging to objectively quantify brain structure and function in ways that are beginning to be used in biomarker development, noting limitations of the data currently available. The most successful machine learning methods that have been developed and applied to date are discussed. Overall, there is increasing evidence that specific features (for example, functional connectivity, gray matter volume) of brain regions comprising the salience and default mode networks can be used to discriminate ASD from typical development. Brain regions contributing to successful discrimination of ADHD from typical development appear to be more widespread, however there is initial evidence that features derived from frontal and cerebellar regions are most informative for classification. The identification of brain-based biomarkers for ASD and ADHD could potentially assist in objective diagnosis, monitoring of treatment response and prediction of outcomes for children with these neurodevelopmental disorders. At present, however, the field has yet to identify reliable and reproducible biomarkers for these disorders, and must address issues related to clinical heterogeneity, methodological standardization and cross-site validation before further progress can be achieved.
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Affiliation(s)
- L Q Uddin
- Department of Psychology, University of Miami, Coral Gables, FL, USA,Neuroscience Program, University of Miami Miller School of Medicine, Miami, FL, USA,Department of Psychology, University of Miami, P.O. Box 248185-0751, Coral Gables, FL 33124, USA. E-mail:
| | - D R Dajani
- Department of Psychology, University of Miami, Coral Gables, FL, USA
| | - W Voorhies
- Department of Psychology, University of Miami, Coral Gables, FL, USA
| | - H Bednarz
- Department of Psychology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - R K Kana
- Department of Psychology, University of Alabama at Birmingham, Birmingham, AL, USA
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Verwaaijen B, Wibberg D, Kröber M, Winkler A, Zrenner R, Bednarz H, Niehaus K, Grosch R, Pühler A, Schlüter A. The Rhizoctonia solani AG1-IB (isolate 7/3/14) transcriptome during interaction with the host plant lettuce (Lactuca sativa L.). PLoS One 2017; 12:e0177278. [PMID: 28486484 PMCID: PMC5423683 DOI: 10.1371/journal.pone.0177278] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 02/16/2017] [Accepted: 04/25/2017] [Indexed: 12/19/2022] Open
Abstract
The necrotrophic pathogen Rhizoctonia solani is one of the most economically important soil-borne pathogens of crop plants. Isolates of R. solani AG1-IB are the major pathogens responsible for bottom-rot of lettuce (Lactuca sativa L.) and are also responsible for diseases in other plant species. Currently, there is lack of information regarding the molecular responses in R. solani during the pathogenic interaction between the necrotrophic soil-borne pathogen and its host plant. The genome of R. solani AG1-IB (isolate 7/3/14) was recently established to obtain insights into its putative pathogenicity determinants. In this study, the transcriptional activity of R. solani AG1-IB was followed during the course of its pathogenic interaction with the host plant lettuce under controlled conditions. Based on visual observations, three distinct pathogen-host interaction zones on lettuce leaves were defined which covered different phases of disease progression on tissue inoculated with the AG1-IB (isolate 7/3/14). The zones were defined as: Zone 1-symptomless, Zone 2-light brown discoloration, and Zone 3-dark brown, necrotic lesions. Differences in R. solani hyphae structure in these three zones were investigated by microscopic observation. Transcriptional activity within these three interaction zones was used to represent the course of R. solani disease progression applying high-throughput RNA sequencing (RNA-Seq) analysis of samples collected from each Zone. The resulting three transcriptome data sets were analyzed for their highest expressed genes and for differentially transcribed genes between the respective interaction zones. Among the highest expressed genes was a group of not previously described genes which were transcribed exclusively during early stages of interaction, in Zones 1 and 2. Previously described importance of up-regulation in R. solani agglutinin genes during disease progression could be further confirmed; here, the corresponding genes exhibited extremely high transcription levels. Most differentially higher expressed transcripts were found within Zone 2. In Zone 3, the zone with the strongest degree of interaction, gene transcripts indicative of apoptotic activity were highly abundant. The transcriptome data presented in this work support previous models of the disease and interaction cycle of R. solani and lettuce and may influence effective techniques for control of this pathogen.
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Affiliation(s)
- Bart Verwaaijen
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Daniel Wibberg
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Magdalena Kröber
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Anika Winkler
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Rita Zrenner
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Hanna Bednarz
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Rita Grosch
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Alfred Pühler
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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Humbert P, Vemmer M, Giampà M, Bednarz H, Niehaus K, Patel AV. Co-encapsulation of amyloglucosidase with starch and Saccharomyces cerevisiae as basis for a long-lasting CO 2 release. World J Microbiol Biotechnol 2017; 33:71. [PMID: 28289929 DOI: 10.1007/s11274-017-2237-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 03/01/2017] [Indexed: 12/01/2022]
Abstract
CO2 is known as a major attractant for many arthropod pests which can be exploited for pest control within novel attract-and-kill strategies. This study reports on the development of a slow-release system for CO2 based on calcium alginate beads containing granular corn starch, amyloglucosidase and Saccharomyces cerevisiae. Our aim was to evaluate the conditions which influence the CO2 release and to clarify the biochemical reactions taking place within the beads. The amyloglucosidase was immobilized with a high encapsulation efficiency of 87% in Ca-alginate beads supplemented with corn starch and S. cerevisiae biomass. The CO2 release from the beads was shown to be significantly affected by the concentration of amyloglucosidase and corn starch within the beads as well as by the incubation temperature. Beads prepared with 0.1 amyloglucosidase units/g matrix solution led to a long-lasting CO2 emission at temperatures between 6 and 25 °C. Starch degradation data correlated well with the CO2 release from beads during incubation and scanning electron microscopy micrographs visualized the degradation of corn starch granules by the co-encapsulated amyloglucosidase. By implementing MALDI-ToF mass spectrometry imaging for the analysis of Ca-alginate beads, we verified that the encapsulated amyloglucosidase converts starch into glucose which is immediately consumed by S. cerevisiae cells. When applied into the soil, the beads increased the CO2 concentration in soil significantly. Finally, we demonstrated that dried beads showed a CO2 production in soil comparable to the moist beads. The long-lasting CO2-releasing beads will pave the way towards novel attract-and-kill strategies in pest control.
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Affiliation(s)
- Pascal Humbert
- Faculty of Engineering and Mathematics, Fermentation and Formulation of Biologicals and Chemicals, Bielefeld University of Applied Sciences, Interaktion 1, 33619, Bielefeld, Germany
| | - Marina Vemmer
- Faculty of Engineering and Mathematics, Fermentation and Formulation of Biologicals and Chemicals, Bielefeld University of Applied Sciences, Interaktion 1, 33619, Bielefeld, Germany
| | - Marco Giampà
- Faculty of Biology, Center for Biotechnology (CeBiTec), Proteome and Metabolome Research, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Hanna Bednarz
- Faculty of Biology, Center for Biotechnology (CeBiTec), Proteome and Metabolome Research, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Karsten Niehaus
- Faculty of Biology, Center for Biotechnology (CeBiTec), Proteome and Metabolome Research, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Anant V Patel
- Faculty of Engineering and Mathematics, Fermentation and Formulation of Biologicals and Chemicals, Bielefeld University of Applied Sciences, Interaktion 1, 33619, Bielefeld, Germany.
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Steffens T, Duda K, Lindner B, Vorhölter FJ, Bednarz H, Niehaus K, Holst O. The lipopolysaccharide of the crop pathogen Xanthomonas translucens pv. translucens: chemical characterization and determination of signaling events in plant cells. Glycobiology 2017; 27:264-274. [PMID: 28177490 DOI: 10.1093/glycob/cww093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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: 06/20/2016] [Revised: 08/29/2016] [Accepted: 08/29/2016] [Indexed: 12/23/2022] Open
Abstract
Xanthomonas translucens pv. translucens (Xtt) is a Gram-negative pathogen of crops from the plant family Poaceae. The lipopolysaccharide (LPS) of Xtt was isolated and chemically characterized. The analyses revealed the presence of rhamnose, xylose, mannose, glucose, galacturonic acid, phosphates, 3-deoxy-D-manno-oct-2-ulopyranosonic acid (Kdo) and fatty acids (10:0, 11:0, 11:0(3-OH) i/a, 11:0(3-OH), 12:0(3-OH) i/a, 12:0(3-OH), 12:0, 13:0(3-OH) i, 13:0(3-OH) a, 13:0(3-OH), 14:0(3-OH) i/a, 14:0(3-OH) and 16:0). The rough type of LPS (lipooligosaccharides; LOS) was isolated and its composition determined utilizing mass spectrometry. The structure of core-lipid A backbone was revealed by nuclear magnetic resonance (NMR) spectroscopy performed on O-deacylated LOS sample, and was shown to be: α-D-Manp-(1→3)-α-D-Manp-(1→3)-β-D-Glcp-(1→4)-α-D-Manp-(1→5)-α-Kdo-(2→6)-β-D-GlcpN-(1→6)-α-D-GlcpN. 4-α-Man and Kdo were further substituted via phosphodiester groups by two galactopyranuronic acids. Xtt LPS elicited a stress response in Nicotiana tabacum suspension cell cultures, namely a transient calcium signal and the generation of H2O2 was observed. Pharmacological studies indicated the involvement of plasma membrane calcium channels, kinases and phospholipase C as key factors in Xtt LPS induced pathogen signaling.
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Affiliation(s)
- Tim Steffens
- Abteilung 27, Proteom- und Metabolomforschung, Fakultät für Biologie & Centre for Biotechnology (CeBiTec) Universität Bielefeld, 33615 Bielefeld, Germany
| | - Katarzyna Duda
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Airway Research Center North (ARCN), German Center for Lung Research, 23845 Borstel, Germany
| | - Buko Lindner
- Division of Immunochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, 23845 Borstel, Germany
| | - Frank-Jörg Vorhölter
- Abteilung 27, Proteom- und Metabolomforschung, Fakultät für Biologie & Centre for Biotechnology (CeBiTec) Universität Bielefeld, 33615 Bielefeld, Germany
| | - Hanna Bednarz
- Abteilung 27, Proteom- und Metabolomforschung, Fakultät für Biologie & Centre for Biotechnology (CeBiTec) Universität Bielefeld, 33615 Bielefeld, Germany
| | - Karsten Niehaus
- Abteilung 27, Proteom- und Metabolomforschung, Fakultät für Biologie & Centre for Biotechnology (CeBiTec) Universität Bielefeld, 33615 Bielefeld, Germany
| | - Otto Holst
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Airway Research Center North (ARCN), German Center for Lung Research, 23845 Borstel, Germany
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Teckentrup J, Al-Hammood O, Steffens T, Bednarz H, Walhorn V, Niehaus K, Anselmetti D. Comparative analysis of different xanthan samples by atomic force microscopy. J Biotechnol 2016; 257:2-8. [PMID: 27919690 DOI: 10.1016/j.jbiotec.2016.11.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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] [Received: 10/06/2016] [Revised: 11/30/2016] [Accepted: 11/30/2016] [Indexed: 02/04/2023]
Abstract
The polysaccharide xanthan which is produced by the γ-proteobacterium Xanthomonas campestris is used as a food thickening agent and rheologic modifier in numerous food, cosmetics and technical applications. Its great commercial importance stimulated biotechnological approaches to optimize the xanthan production. By targeted genetic modification the metabolism of Xanthomonas can be modified in such a way that the xanthan production efficiency and/or the shear-thickening potency is optimized. Using atomic force microscopy (AFM) the secondary structure of single xanthan polymers produced by the wild type Xanthomonas campestris B100 and several genetically modified variations were analyzed. We found a wide variation of characteristic differences between xanthan molecules produced by different strains. The structures ranged from single-stranded coiled polymers to branched xanthan double-strands. These results can help to get a better understanding of the polymerization- and secretion-machinery that are relevant for xanthan synthesis. Furthermore, we demonstrate that the xanthan secondary structure strongly correlates with its viscosifying properties.
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Affiliation(s)
- Julia Teckentrup
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Germany.
| | - Orooba Al-Hammood
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Germany.
| | - Tim Steffens
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Germany.
| | - Hanna Bednarz
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Germany.
| | - Volker Walhorn
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Germany.
| | - Karsten Niehaus
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Germany.
| | - Dario Anselmetti
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Germany.
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31
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Gren T, Ortseifen V, Wibberg D, Schneiker-Bekel S, Bednarz H, Niehaus K, Zemke T, Persicke M, Pühler A, Kalinowski J. Genetic engineering in Actinoplanes sp. SE50/110 − development of an intergeneric conjugation system for the introduction of actinophage-based integrative vectors. J Biotechnol 2016; 232:79-88. [DOI: 10.1016/j.jbiotec.2016.05.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 05/06/2016] [Accepted: 05/11/2016] [Indexed: 01/10/2023]
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32
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Giampà M, Lissel MB, Patschkowski T, Fuchser J, Hans VH, Gembruch O, Bednarz H, Niehaus K. Maleic anhydride proton sponge as a novel MALDI matrix for the visualization of small molecules (<250 m/z) in brain tumors by routine MALDI ToF imaging mass spectrometry. Chem Commun (Camb) 2016; 52:9801-4. [DOI: 10.1039/c6cc02387h] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A novel MALDI matrix MAPS, able to visualize deviating metabolism in glioma using a routine MALDI-ToF-MSI procedure, is presented.
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Affiliation(s)
- M. Giampà
- Center for Biotechnology and Department for Proteome and Metabolome Research
- Faculty of Biology
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - M. B. Lissel
- Center for Biotechnology and Department for Proteome and Metabolome Research
- Faculty of Biology
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - T. Patschkowski
- Center for Biotechnology and Department for Proteome and Metabolome Research
- Faculty of Biology
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - J. Fuchser
- Bruker Daltonics GmbH
- BU Pharma
- 28259 Bremen
- Germany
| | - V. H. Hans
- Institut für Pathologie Ruhr-Universität Bochum
- 44789 Bochum
- Germany
- Institut für Neuropathologie
- Universitätsklinikum Essen (AöR)
| | - O. Gembruch
- Klinik für Neurochirurgie
- Universitätsklinikum Essen (AöR)
- 45147 Essen
- Germany
| | - H. Bednarz
- Center for Biotechnology and Department for Proteome and Metabolome Research
- Faculty of Biology
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - K. Niehaus
- Center for Biotechnology and Department for Proteome and Metabolome Research
- Faculty of Biology
- Bielefeld University
- 33615 Bielefeld
- Germany
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Freudenau I, Lutter P, Baier R, Schleef M, Bednarz H, Lara AR, Niehaus K. ColE1-Plasmid Production in Escherichia coli: Mathematical Simulation and Experimental Validation. Front Bioeng Biotechnol 2015; 3:127. [PMID: 26389114 PMCID: PMC4555960 DOI: 10.3389/fbioe.2015.00127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 06/05/2015] [Accepted: 08/13/2015] [Indexed: 12/15/2022] Open
Abstract
Plasmids have become very important as pharmaceutical gene vectors in the fields of gene therapy and genetic vaccination in the past years. In this study, we present a dynamic model to simulate the ColE1-like plasmid replication control, once for a DH5α-strain carrying a low copy plasmid (DH5α-pSUP 201-3) and once for a DH5α-strain carrying a high copy plasmid (DH5α-pCMV-lacZ) by using ordinary differential equations and the MATLAB software. The model includes the plasmid replication control by two regulatory RNA molecules (RNAI and RNAII) as well as the replication control by uncharged tRNA molecules. To validate the model, experimental data like RNAI- and RNAII concentration, plasmid copy number (PCN), and growth rate for three different time points in the exponential phase were determined. Depending on the sampled time point, the measured RNAI- and RNAII concentrations for DH5α-pSUP 201-3 reside between 6 ± 0.7 and 34 ± 7 RNAI molecules per cell and 0.44 ± 0.1 and 3 ± 0.9 RNAII molecules per cell. The determined PCNs averaged between 46 ± 26 and 48 ± 30 plasmids per cell. The experimentally determined data for DH5α-pCMV-lacZ reside between 345 ± 203 and 1086 ± 298 RNAI molecules per cell and 22 ± 2 and 75 ± 10 RNAII molecules per cell with an averaged PCN of 1514 ± 1301 and 5806 ± 4828 depending on the measured time point. As the model was shown to be consistent with the experimentally determined data, measured at three different time points within the growth of the same strain, we performed predictive simulations concerning the effect of uncharged tRNA molecules on the ColE1-like plasmid replication control. The hypothesis is that these tRNA molecules would have an enhancing effect on the plasmid production. The in silico analysis predicts that uncharged tRNA molecules would indeed increase the plasmid DNA production.
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Affiliation(s)
- Inga Freudenau
- Abteilung für Proteom- und Metabolomforschung, Fakultät für Biologie, Universität Bielefeld, Bielefeld, Germany
| | - Petra Lutter
- Abteilung für Proteom- und Metabolomforschung, Fakultät für Biologie, Universität Bielefeld, Bielefeld, Germany
| | - Ruth Baier
- PlasmidFactory GmbH & Co. KG, Bielefeld, Germany
| | | | - Hanna Bednarz
- Abteilung für Proteom- und Metabolomforschung, Fakultät für Biologie, Universität Bielefeld, Bielefeld, Germany
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Alvaro R. Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
| | - Karsten Niehaus
- Abteilung für Proteom- und Metabolomforschung, Fakultät für Biologie, Universität Bielefeld, Bielefeld, Germany
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
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Winkelmann T, Ratjens S, Bartsch M, Rode C, Niehaus K, Bednarz H. Metabolite profiling of somatic embryos of Cyclamen persicum in comparison to zygotic embryos, endosperm, and testa. Front Plant Sci 2015; 6:597. [PMID: 26300898 PMCID: PMC4523879 DOI: 10.3389/fpls.2015.00597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 07/20/2015] [Indexed: 05/29/2023]
Abstract
Somatic embryogenesis has been shown to be an efficient in vitro plant regeneration system for many crops such as the important ornamental plant Cyclamen persicum, for which this regeneration pathway of somatic embryogenesis is of interest for the vegetative propagation of parental lines as well as elite plants. However, somatic embryogenesis is not commercially used in many crops due to several unsolved problems, such as malformations, asynchronous development, deficiencies in maturation and germination of somatic embryos. In contrast, zygotic embryos in seeds develop and germinate without abnormalities in most cases. Instead of time-consuming and labor-intensive experiments involving tests of different in vitro culture conditions and plant growth regulator supplements, we follow a more directed approach. Zygotic embryos served as a reference and were compared to somatic embryos in metabolomic analyses allowing the future optimization of the in vitro system. The aims of this study were to detect differences in the metabolite profiles of torpedo stage somatic and zygotic embryos of C. persicum. Moreover, major metabolites in endosperm and testa were identified and quantified. Two sets of extracts of two to four biological replicates each were analyzed. In total 52 metabolites were identified and quantified in the different tissues. One of the most significant differences between somatic and zygotic embryos was that the proline concentration in the zygotic embryos was about 40 times higher than that found in somatic embryos. Epicatechin, a scavenger for reactive oxygen species, was found in highest abundance in the testa. Sucrose, the most abundant metabolite was detected in significantly higher concentrations in zygotic embryos. Also, a yet unknown trisaccharide, was significantly enriched in zygotic embryos.
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Affiliation(s)
- Traud Winkelmann
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
| | - Svenja Ratjens
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
| | - Melanie Bartsch
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
| | - Christina Rode
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
| | - Karsten Niehaus
- Faculty of Biology, Bio 27, Proteome and Metabolome Research, Bielefeld UniversityBielefeld, Germany
| | - Hanna Bednarz
- Faculty of Biology, Bio 27, Proteome and Metabolome Research, Bielefeld UniversityBielefeld, Germany
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Persicke M, Albersmeier A, Bednarz H, Niehaus K, Kalinowski J, Rückert C. Genome sequence of the soil bacterium Corynebacterium callunae type strain DSM 20147(T). Stand Genomic Sci 2015. [PMID: 26203323 PMCID: PMC4510995 DOI: 10.1186/1944-3277-10-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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] [Indexed: 11/23/2022] Open
Abstract
Corynebacterium callunae DSM 20147T is a member of the genus Corynebacterium which contains Gram-positive and non-spore forming bacteria with a high G + C content. C. callunae was isolated during a screening for l-glutamic acid producing bacteria and belongs to the aerobic and non-haemolytic corynebacteria. As this is a type strain in a subgroup of industrial relevant bacteria for many of which there are also complete genome sequence available, knowledge of the complete genome sequence might enable genome comparisons to identify production relevant genetic loci. This project, describing the 2.84 Mbp long chromosome and the two plasmids, pCC1 (4.11 kbp) and pCC2 (85.02 kbp), with their 2,647 protein-coding and 82 RNA genes, will aid the Genomic Encyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Marcus Persicke
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Andreas Albersmeier
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
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Aladedunye F, Przybylski R, Niehaus K, Bednarz H, Matthäus B. Phenolic extracts from Crataegus × mordenensis and Prunus virginiana: Composition, antioxidant activity and performance in sunflower oil. Lebensm Wiss Technol 2014. [DOI: 10.1016/j.lwt.2014.06.002] [Citation(s) in RCA: 11] [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: 10/25/2022]
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37
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Al-Dilaimi A, Bednarz H, Lömker A, Niehaus K, Kalinowski J, Rückert C. Revisiting Corynebacterium glyciniphilum (ex Kubota et al., 1972) sp. nov., nom. rev., isolated from putrefied banana. Int J Syst Evol Microbiol 2014; 65:177-182. [PMID: 25323597 DOI: 10.1099/ijs.0.065102-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strain of a species of the genus Corynebacterium, designated AJ 3170(T), was isolated during the 1980s from putrefied bananas. Since then, there have been no further updates on the description of the strain or its phylogenetic classification. However, phylogenetic analysis of this strain using 16S rRNA and in silico DNA-DNA hybridization has confirmed that it is a member of the genus Corynebacterium and that strain AJ 3170(T) clusters with Corynebacterium variabile DSM 44702(T), Corynebacterium terpenotabidum Y-11(T) and Corynebacterium nuruki S6-4(T) in one subgroup. Furthermore, a combination of enzymatic, chemical, and morphological characterization techniques was applied in order to describe strain AJ 3170(T) further. The strain grew well at pH values of 6-10 and at temperatures of 30-41 °C. The major fatty acids were C16 : 0 (42.15 %), C18 : 1ω9c (41.6 %) and C18 : 0 10-methyl (TBSA) (8.56 %). The whole-cell sugars were determined to comprise galactose, arabinose and ribose. On the basis of this phenotypic, chemotaxonomic and phylogenetic characterization, it is proposed that strain AJ 3170(T) represents a novel species, for which the name Corynebacterium glyciniphilum sp. nov. is proposed; the type strain is AJ 3170(T) ( = DSM 45795(T) = ATCC 21341(T)).
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Affiliation(s)
- Arwa Al-Dilaimi
- Microbial Genomics and Biotechnology, CeBiTec, Bielefeld University, D-33615 Bielefeld, Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Bielefeld University, D-33615 Bielefeld, Germany
| | - Alexander Lömker
- Microbial Genomics and Biotechnology, CeBiTec, Bielefeld University, D-33615 Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Bielefeld University, D-33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, D-33615 Bielefeld, Germany.,Microbial Genomics and Biotechnology, CeBiTec, Bielefeld University, D-33615 Bielefeld, Germany
| | - Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, D-33615 Bielefeld, Germany.,Microbial Genomics and Biotechnology, CeBiTec, Bielefeld University, D-33615 Bielefeld, Germany
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Patel A, Spieth P, Bednarz H, Niehaus K, Lohse R. Können Endophyten eines tropischen Baumes Bioinsektizide produzieren? CHEM-ING-TECH 2014. [DOI: 10.1002/cite.201450062] [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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39
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Rückert C, Albersmeier A, Al-Dilaimi A, Bednarz H, Niehaus K, Szczepanowski R, Kalinowski J. Genome sequence of the squalene-degrading bacterium Corynebacterium terpenotabidum type strain Y-11(T) (= DSM 44721(T)). Stand Genomic Sci 2014; 9:505-13. [PMID: 25197436 PMCID: PMC4149027 DOI: 10.4056/sigs.4588337] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [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] [Indexed: 01/30/2023] Open
Abstract
Corynebacterium terpenotabidum Takeuchi et. al 1999 is a member of the genus Corynebacterium, which contains Gram-positive and non-spore forming bacteria with a high G+C content. C. terpenotabidum was isolated from soil based on its ability to degrade squalene and belongs to the aerobic and non-hemolytic Corynebacteria. It displays tolerance to salts (up to 8%) and is related to Corynebacterium variabile involved in cheese ripening. As this is a type strain of Corynebacterium, this project describing the 2.75 Mbp long chromosome with its 2,369 protein-coding and 72 RNA genes will aid the G enomic E ncyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Andreas Albersmeier
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Arwa Al-Dilaimi
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | | | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
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Gorzolka K, Bednarz H, Niehaus K. Detection and localization of novel hordatine-like compounds and glycosylated derivates of hordatines by imaging mass spectrometry of barley seeds. Planta 2014; 239:1321-35. [PMID: 24671626 DOI: 10.1007/s00425-014-2061-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 03/06/2014] [Indexed: 05/22/2023]
Abstract
Mass spectrometry imaging was applied on germinated barley for the detailed localization of metabolites in longitudinal and transversal seed sections. Among others, 20 m/z signals occurred in three regular peak clusters with specific, distinct localizations in embryo tissues. High resolution FT-ICR MS, MALDI-TOF MS/MS, and UHPLC-ESI MS/MS served for the identification and structural characterization of these compounds. Only five metabolites were published in their structures, namely the antifungal compounds hordatine A and B in non-glycosylated and glycosylated forms. All other non-identified cluster compounds were of hordatine-like structure and differed by systematic O-methylations, hydroxylations, and glycosylations. These differences in molecular structures correlated to distinct localization patterns within the embryo and might serve for the regulation of antifungal properties. Based on the structural investigations by mass spectrometry, an array of different hordatines that comprises the five published hordatines, 15 novel hordatine derivates and their six precursors could be localized in the embryo of germinated barley. Implications for the biosynthetic pathway and transport processes are discussed.
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Affiliation(s)
- Karin Gorzolka
- Proteome and Metabolome Research, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstraße 25, 33615, Bielefeld, Germany,
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Schaffert L, Albersmeier A, Bednarz H, Niehaus K, Kalinowski J, Rückert C. Genome sequence of the marine bacterium Corynebacterium maris type strain Coryn-1(T) (= DSM 45190(T)). Stand Genomic Sci 2013; 8:516-24. [PMID: 24501635 PMCID: PMC3910691 DOI: 10.4056/sigs.4057796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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] [Indexed: 11/20/2022] Open
Abstract
Corynebacterium maris Coryn-1(T) Ben-Dov et al. 2009 is a member of the genus Corynebacterium which contains Gram-positive, non-spore forming bacteria with a high G+C content. C. maris was isolated from the mucus of the Scleractinian coral Fungia granulosa and belongs to the aerobic and non-haemolytic corynebacteria. It displays tolerance to salts (up to 10%) and is related to the soil bacterium Corynebacterium halotolerans. As this is a type strain in a subgroup of Corynebacterium without complete genome sequences, this project, describing the 2.78 Mbp long chromosome and the 45.97 kbp plasmid pCmaris1, with their 2,584 protein-coding and 67 RNA genes, will aid the G enomic E ncyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Lena Schaffert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Andreas Albersmeier
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
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