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Wang Q, Lechtenfeld OJ, Rietveld LC, Schuster J, Ernst M, Hofman-Caris R, Kaesler J, Wang C, Yang M, Yu J, Zietzschmann F. How aromatic dissolved organic matter differs in competitiveness against organic micropollutant adsorption. Environ Sci Ecotechnol 2024; 21:100392. [PMID: 38434492 PMCID: PMC10907174 DOI: 10.1016/j.ese.2024.100392] [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] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/11/2024] [Accepted: 01/14/2024] [Indexed: 03/05/2024]
Abstract
Activated carbon is employed for the adsorption of organic micropollutants (OMPs) from water, typically present in concentrations ranging from ng L-1 to μg L-1. However, the efficacy of OMP removal is considerably deteriorated due to competitive adsorption from background dissolved organic matter (DOM), present at substantially higher concentrations in mg L-1. Interpreting the characteristics of competitive DOM is crucial in predicting OMP adsorption efficiencies across diverse natural waters. Molecular weight (MW), aromaticity, and polarity influence DOM competitiveness. Although the aromaticity-related metrics, such as UV254, of low MW DOM were proposed to correlate with DOM competitiveness, the method suffers from limitations in understanding the interplay of polarity and aromaticity in determining DOM competitiveness. Here, we elucidate the intricate influence of aromaticity and polarity in low MW DOM competition, spanning from a fraction level to a compound level, by employing direct sample injection liquid chromatography coupled with ultrahigh-resolution Fourier-transform ion cyclotron resonance mass spectrometry. Anion exchange resin pre-treatment eliminated 93% of UV254-active DOM, predominantly aromatic and polar DOM, and only minimally alleviated DOM competition. Molecular characterization revealed that nonpolar molecular formulas (constituting 26% PAC-adsorbable DOM) with medium aromaticity contributed more to the DOM competitiveness. Isomer-level analysis indicated that the competitiveness of highly aromatic LMW DOM compounds was strongly counterbalanced by increased polarity. Strong aromaticity-derived π-π interaction cannot facilitate the competitive adsorption of hydrophilic DOM compounds. Our results underscore the constraints of depending solely on aromaticity-based approaches as the exclusive interpretive measure for DOM competitiveness. In a broader context, this study demonstrates an effect-oriented DOM analysis, elucidating counterbalancing interactions of DOM molecular properties from fraction to compound level.
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Affiliation(s)
- Qi Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
- Delft University of Technology, Department of Water Management, PO Box 5048, 2600, GA, Delft, the Netherlands
| | - Oliver J. Lechtenfeld
- Department of Analytical Chemistry, Research Group BioGeoOmics, Helmholtz Centre for Environmental Research − UFZ, Permoserstr. 15, 04318, Leipzig, Germany
- ProVIS−Centre for Chemical Microscopy, Helmholtz Centre for Environmental Research − UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Luuk C. Rietveld
- Delft University of Technology, Department of Water Management, PO Box 5048, 2600, GA, Delft, the Netherlands
| | - Jonas Schuster
- Institute for Water Resources and Water Supply, Hamburg University of Technology, Am Schwarzenberg-Campus 3, 21073, Hamburg, Germany
| | - Mathias Ernst
- Institute for Water Resources and Water Supply, Hamburg University of Technology, Am Schwarzenberg-Campus 3, 21073, Hamburg, Germany
| | - Roberta Hofman-Caris
- KWR Watercycle Research Institute, 3433PE, Nieuwegein, the Netherlands
- Wageningen University and Research, Department of Environmental Technology, Bornse Weilanden 9, 6708 WG, Wageningen, the Netherlands
| | - Jan Kaesler
- Department of Analytical Chemistry, Research Group BioGeoOmics, Helmholtz Centre for Environmental Research − UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Chunmiao Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
| | - Min Yang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jianwei Yu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Frederik Zietzschmann
- Delft University of Technology, Department of Water Management, PO Box 5048, 2600, GA, Delft, the Netherlands
- Berliner Wasserbetriebe, Laboratory, Motardstr. 35, 13629, Berlin, Germany
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2
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Lechtenfeld OJ, Kaesler J, Jennings EK, Koch BP. Direct Analysis of Marine Dissolved Organic Matter Using LC-FT-ICR MS. Environ Sci Technol 2024; 58:4637-4647. [PMID: 38427796 PMCID: PMC10938638 DOI: 10.1021/acs.est.3c07219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/20/2024] [Accepted: 02/07/2024] [Indexed: 03/03/2024]
Abstract
Marine dissolved organic matter (DOM) is an important component of the global carbon cycle, yet its intricate composition and the sea salt matrix pose major challenges for chemical analysis. We introduce a direct injection, reversed-phase liquid chromatography ultrahigh resolution mass spectrometry approach to analyze marine DOM without the need for solid-phase extraction. Effective separation of salt and DOM is achieved with a large chromatographic column and an extended isocratic aqueous step. Postcolumn dilution of the sample flow with buffer-free solvents and implementing a counter gradient reduced salt buildup in the ion source and resulted in excellent repeatability. With this method, over 5,500 unique molecular formulas were detected from just 5.5 nmol carbon in 100 μL of filtered Arctic Ocean seawater. We observed a highly linear detector response for variable sample carbon concentrations and a high robustness against the salt matrix. Compared to solid-phase extracted DOM, our direct injection method demonstrated superior sensitivity for heteroatom-containing DOM. The direct analysis of seawater offers fast and simple sample preparation and avoids fractionation introduced by extraction. The method facilitates studies in environments, where only minimal sample volume is available e.g. in marine sediment pore water, ice cores, or permafrost soil solution. The small volume requirement also supports higher spatial (e.g., in soils) or temporal sample resolution (e.g., in culture experiments). Chromatographic separation adds further chemical information to molecular formulas, enhancing our understanding of marine biogeochemistry, chemodiversity, and ecological processes.
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Affiliation(s)
- Oliver J. Lechtenfeld
- Department
of Environmental Analytical Chemistry, Research Group BioGeoOmics, Helmholtz Centre for Environmental Research −
UFZ, Permoserstraße
15, 04318 Leipzig, Germany
- ProVIS−Centre
for Chemical Microscopy, Helmholtz Centre
for Environmental Research − UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Jan Kaesler
- Department
of Environmental Analytical Chemistry, Research Group BioGeoOmics, Helmholtz Centre for Environmental Research −
UFZ, Permoserstraße
15, 04318 Leipzig, Germany
| | - Elaine K. Jennings
- Department
of Environmental Analytical Chemistry, Research Group BioGeoOmics, Helmholtz Centre for Environmental Research −
UFZ, Permoserstraße
15, 04318 Leipzig, Germany
| | - Boris P. Koch
- Alfred-Wegener-Institut
Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany
- University
of Applied Sciences, An der Karlstadt 8, 27568 Bremerhaven, Germany
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3
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Pertzborn D, Arolt C, Ernst G, Lechtenfeld OJ, Kaesler J, Pelzel D, Guntinas-Lichius O, von Eggeling F, Hoffmann F. Multi-Class Cancer Subtyping in Salivary Gland Carcinomas with MALDI Imaging and Deep Learning. Cancers (Basel) 2022; 14:cancers14174342. [PMID: 36077876 PMCID: PMC9454426 DOI: 10.3390/cancers14174342] [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] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/18/2022] [Accepted: 09/03/2022] [Indexed: 11/16/2022] Open
Abstract
Salivary gland carcinomas (SGC) are a heterogeneous group of tumors. The prognosis varies strongly according to its type, and even the distinction between benign and malign tumor is challenging. Adenoid cystic carcinoma (AdCy) is one subgroup of SGCs that is prone to late metastasis. This makes accurate tumor subtyping an important task. Matrix-assisted laser desorption/ionization (MALDI) imaging is a label-free technique capable of providing spatially resolved information about the abundance of biomolecules according to their mass-to-charge ratio. We analyzed tissue micro arrays (TMAs) of 25 patients (including six different SGC subtypes and a healthy control group of six patients) with high mass resolution MALDI imaging using a 12-Tesla magnetic resonance mass spectrometer. The high mass resolution allowed us to accurately detect single masses, with strong contributions to each class prediction. To address the added complexity created by the high mass resolution and multiple classes, we propose a deep-learning model. We showed that our deep-learning model provides a per-class classification accuracy of greater than 80% with little preprocessing. Based on this classification, we employed methods of explainable artificial intelligence (AI) to gain further insights into the spectrometric features of AdCys.
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Affiliation(s)
- David Pertzborn
- Innovative Biophotonics & MALDI Imaging, ENT Department, Jena University Hospital, 07747 Jena, Germany
| | - Christoph Arolt
- Institute of Pathology, Medical Faculty, University of Cologne, 50937 Cologne, Germany
| | - Günther Ernst
- Innovative Biophotonics & MALDI Imaging, ENT Department, Jena University Hospital, 07747 Jena, Germany
| | - Oliver J. Lechtenfeld
- Department of Analytical Chemistry, Research Group BioGeoOmics, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany
- ProVIS−Centre for Chemical Microscopy, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany
| | - Jan Kaesler
- Department of Analytical Chemistry, Research Group BioGeoOmics, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany
| | - Daniela Pelzel
- Innovative Biophotonics & MALDI Imaging, ENT Department, Jena University Hospital, 07747 Jena, Germany
| | - Orlando Guntinas-Lichius
- Innovative Biophotonics & MALDI Imaging, ENT Department, Jena University Hospital, 07747 Jena, Germany
| | - Ferdinand von Eggeling
- Innovative Biophotonics & MALDI Imaging, ENT Department, Jena University Hospital, 07747 Jena, Germany
| | - Franziska Hoffmann
- Innovative Biophotonics & MALDI Imaging, ENT Department, Jena University Hospital, 07747 Jena, Germany
- Correspondence:
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Han L, Kaesler J, Peng C, Reemtsma T, Lechtenfeld OJ. Online Counter Gradient LC-FT-ICR-MS Enables Detection of Highly Polar Natural Organic Matter Fractions. Anal Chem 2021; 93:1740-1748. [PMID: 33370097 DOI: 10.1021/acs.analchem.0c04426] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural organic matter (NOM) is a highly complex mixture of natural organic molecules. The recent developments in NOM molecular characterization methods have shown that ESI-FT-ICR hyphenated with liquid chromatography (LC) is a promising approach to also obtain chemical information (such as polarity and molecular size) about NOM molecules. However, due to changing solvent composition during gradient elution in LC-FT-ICR-MS, ionization conditions also change throughout the chromatographic separation process. In this study, we applied a post-LC column counter gradient (CG) to ensure stable solvent conditions for transient ESI-MS signals. Suwanee River Fulvic Acid (SRFA) standard and a peat pore water were used as representative dissolved NOM samples for method development and validation. Our results show that in polar NOM fractions (which elute with <50% methanol) the TIC intensity and number of assigned molecular formulas were increased by 48% and 20%, as compared to the standard gradient (SG) method. Further application of a Q-isolation and selective ion accumulation for low abundance fractions revealed over 3 times more molecular formulas (especially for CHNO, CHOS, CHNOS formula classes) than in full scan mode. The number of detected highly polar NOM compounds (with elemental ratios H/C < 1, O/C > 0.6) were more than 20 times larger for CG-LC mode as compared to direct infusion (DI) (5715 vs 266 MF). We conclude that the application of a postcolumn counter gradient in LC-FT-ICR-MS analyses of NOM offers novel insight into the most polar fractions of NOM which are inaccessible in conventional DI measurements.
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Affiliation(s)
- Limei Han
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany
| | - Jan Kaesler
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany
| | - Chang Peng
- Institute of Analytical Chemistry, University of Leipzig, 04103 Leipzig, Germany
| | - Thorsten Reemtsma
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany.,Institute of Analytical Chemistry, University of Leipzig, 04103 Leipzig, Germany
| | - Oliver J Lechtenfeld
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany.,ProVIS-Centre for Chemical Microscopy, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany
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5
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Hons MT, Huis in ‘t Veld PJ, Kaesler J, Rombaut P, Schleiffer A, Herzog F, Stark H, Peters JM. Topology and structure of an engineered human cohesin complex bound to Pds5B. Nat Commun 2016; 7:12523. [PMID: 27549742 PMCID: PMC4996973 DOI: 10.1038/ncomms12523] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 07/12/2016] [Indexed: 12/19/2022] Open
Abstract
The cohesin subunits Smc1, Smc3 and Scc1 form large tripartite rings which mediate sister chromatid cohesion and chromatin structure. These are thought to entrap DNA with the help of the associated proteins SA1/2 and Pds5A/B. Structural information is available for parts of cohesin, but analyses of entire cohesin complexes are limited by their flexibility. Here we generated a more rigid 'bonsai' cohesin by truncating the coiled coils of Smc1 and Smc3 and used single-particle electron microscopy, chemical crosslinking-mass spectrometry and in silico modelling to generate three-dimensional models of cohesin bound to Pds5B. The HEAT-repeat protein Pds5B forms a curved structure around the nucleotide-binding domains of Smc1 and Smc3 and bridges the Smc3-Scc1 and SA1-Scc1 interfaces. These results indicate that Pds5B forms an integral part of the cohesin ring by contacting all other cohesin subunits, a property that may reflect the complex role of Pds5 proteins in controlling cohesin-DNA interactions.
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Affiliation(s)
- Michael T. Hons
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | | | - Jan Kaesler
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Pascaline Rombaut
- Department of Biochemistry, Gene Center, Ludwig-Maximilian University, Feodor-Lynen-Strasse 25, Munich 81377, Germany
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Dr Bohr-Gasse 7, Vienna 1030, Austria
| | - Franz Herzog
- Department of Biochemistry, Gene Center, Ludwig-Maximilian University, Feodor-Lynen-Strasse 25, Munich 81377, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Dr Bohr-Gasse 7, Vienna 1030, Austria
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6
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Gundlach J, Dickmanns A, Schröder-Tittmann K, Neumann P, Kaesler J, Kampf J, Herzberg C, Hammer E, Schwede F, Kaever V, Tittmann K, Stülke J, Ficner R. Identification, characterization, and structure analysis of the cyclic di-AMP-binding PII-like signal transduction protein DarA. J Biol Chem 2014; 290:3069-80. [PMID: 25433025 DOI: 10.1074/jbc.m114.619619] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The cyclic dimeric AMP nucleotide c-di-AMP is an essential second messenger in Bacillus subtilis. We have identified the protein DarA as one of the prominent c-di-AMP receptors in B. subtilis. Crystal structure analysis shows that DarA is highly homologous to PII signal transducer proteins. In contrast to PII proteins, the functionally important B- and T-loops are swapped with respect to their size. DarA is a homotrimer that binds three molecules of c-di-AMP, each in a pocket located between two subunits. We demonstrate that DarA is capable to bind c-di-AMP and with lower affinity cyclic GMP-AMP (3'3'-cGAMP) but not c-di-GMP or 2'3'-cGAMP. Consistently the crystal structure shows that within the ligand-binding pocket only one adenine is highly specifically recognized, whereas the pocket for the other adenine appears to be promiscuous. Comparison with a homologous ligand-free DarA structure reveals that c-di-AMP binding is accompanied by conformational changes of both the fold and the position of the B-loop in DarA.
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Affiliation(s)
| | | | | | | | | | - Jan Kampf
- From the Departments of General Microbiology
| | | | - Elke Hammer
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Frank Schwede
- BIOLOG Life Science Institute, 28199 Bremen, Germany, and
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical School, 30625 Hannover, Germany
| | - Kai Tittmann
- Molecular Enzymology, Georg August University Göttingen, 37077 Göttingen, Germany
| | - Jörg Stülke
- From the Departments of General Microbiology,
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