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Krebs P, Nägele M, Fomina P, Virtanen V, Nippolainen E, Shaikh R, Afara I, Töyräs J, Usenov I, Sakharova T, Artyushenko V, Tafintseva V, Solheim J, Zimmermann B, Kohler A, König O, Saarakkala S, Mizaikoff B. Laser-irradiating infrared attenuated total reflection spectroscopy of articular cartilage: Potential and challenges for diagnosing osteoarthritis. Osteoarthr Cartil Open 2024; 6:100466. [PMID: 38623306 PMCID: PMC11016904 DOI: 10.1016/j.ocarto.2024.100466] [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: 09/20/2023] [Accepted: 03/26/2024] [Indexed: 04/17/2024] Open
Abstract
Objective A prototype infrared attenuated total reflection (IR-ATR) laser spectroscopic system designed for in vivo classification of human cartilage tissue according to its histological health status during arthroscopic surgery is presented. Prior to real-world in vivo applications, this so-called osteoarthritis (OA) scanner has been tested at in vitro conditions revealing the challenges associated with complex sample matrices and the accordingly obtained sparse spectral datasets. Methods In vitro studies on human knee cartilage samples at different contact pressures (i.e., 0.2-0.5 MPa) allowed recording cartilage degeneration characteristic IR signatures comparable to in vivo conditions with high temporal resolution. Afterwards, the cartilage samples were assessed based on the clinically acknowledged osteoarthritis cartilage histopathology assessment (OARSI) system and correlated with the obtained sparse IR data. Results Amide and carbohydrate signal behavior was observed to be almost identical between the obtained sparse IR data and previously measured FTIR data used for sparse partial least squares discriminant analysis (SPLSDA) to identify the spectral regions relevant to cartilage condition. Contact pressures between 0.3 and 0.4 MPa seem to provide the best sparse IR spectra for cylindrical (d = 3 mm) probe tips. Conclusion Laser-irradiating IR-ATR spectroscopy is a promising analytical technique for future arthroscopic applications to differentiate healthy and osteoarthritic cartilage tissue. However, this study also revealed that the flexible connection between the laser-based analyzer and the arthroscopic ATR-probe via IR-transparent fiberoptic cables may affect the robustness of the obtained IR data and requires further improvements.
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Affiliation(s)
- P. Krebs
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Ulm, Germany
| | | | - P. Fomina
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Ulm, Germany
| | - V. Virtanen
- Research Unit of Health Sciences and Technology, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - E. Nippolainen
- Department of Technical Physics, University of Eastern Finland, Kuopio, Finland
| | - R. Shaikh
- Department of Technical Physics, University of Eastern Finland, Kuopio, Finland
| | - I.O. Afara
- Department of Technical Physics, University of Eastern Finland, Kuopio, Finland
| | - J. Töyräs
- Department of Technical Physics, University of Eastern Finland, Kuopio, Finland
- Science Service Center, Kuopio University Hospital, Kuopio, Finland
- School of Electrical Engineering and Computer Science, The University of Queensland, Brisbane, Australia
| | | | | | | | - V. Tafintseva
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - J.H. Solheim
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - B. Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - A. Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - O. König
- Nanoplus Advanced Photonics Gerbrunn GmbH, Gerbrunn, Germany
| | - S. Saarakkala
- Research Unit of Health Sciences and Technology, Faculty of Medicine, University of Oulu, Oulu, Finland
- Department of Diagnostic Radiology, Oulu University Hospital, Oulu, Finland
| | - B. Mizaikoff
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Ulm, Germany
- Hahn-Schickard, Ulm, Germany
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Akulava V, Smirnova M, Byrtusova D, Zimmermann B, Ekeberg D, Kohler A, Blazhko U, Miamin U, Valentovich L, Shapaval V. Explorative characterization and taxonomy-aligned comparison of alterations in lipids and other biomolecules in Antarctic bacteria grown at different temperatures. Environ Microbiol Rep 2024; 16:e13232. [PMID: 38308519 PMCID: PMC10878007 DOI: 10.1111/1758-2229.13232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 02/04/2024]
Abstract
Temperature significantly impacts bacterial physiology, metabolism and cell chemistry. In this study, we analysed lipids and the total cellular biochemical profile of 74 fast-growing Antarctic bacteria grown at different temperatures. Fatty acid diversity and temperature-induced alterations aligned with bacterial classification-Gram-groups, phylum, genus and species. Total lipid content, varied from 4% to 19% of cell dry weight, was genus- and species-specific. Most bacteria increased lipid content at lower temperatures. The effect of temperature on the profile was complex and more species-specific, while some common for all bacteria responses were recorded. Gram-negative bacteria adjusted unsaturation and acyl chain length. Gram-positive bacteria adjusted methyl branching (anteiso-/iso-), chain length and unsaturation. Fourier transform infrared spectroscopy analysis revealed Gram-, genus- and species-specific changes in the total cellular biochemical profile triggered by temperature fluctuations. The most significant temperature-related alterations detected on all taxonomy levels were recorded for mixed region 1500-900 cm-1 , specifically the band at 1083 cm-1 related to phosphodiester groups mainly from phospholipids (for Gram-negative bacteria) and teichoic/lipoteichoic acids (for Gram-positive bacteria). Some changes in protein region were detected for a few genera, while the lipid region remained relatively stable despite the temperature fluctuations.
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Affiliation(s)
- Volha Akulava
- Faculty of Science and TechnologyNorwegian University of Life SciencesÅsNorway
| | - Margarita Smirnova
- Faculty of Science and TechnologyNorwegian University of Life SciencesÅsNorway
| | - Dana Byrtusova
- Faculty of Science and TechnologyNorwegian University of Life SciencesÅsNorway
| | - Boris Zimmermann
- Faculty of Science and TechnologyNorwegian University of Life SciencesÅsNorway
| | - Dag Ekeberg
- Faculty of Chemistry, Biotechnology and Food ScienceNorwegian University of Life SciencesÅsNorway
| | - Achim Kohler
- Faculty of Science and TechnologyNorwegian University of Life SciencesÅsNorway
| | - Uladzislau Blazhko
- Faculty of Science and TechnologyNorwegian University of Life SciencesÅsNorway
| | | | - Leonid Valentovich
- Institute of MicrobiologyNational Academy of Sciences of BelarusMinskBelarus
| | - Volha Shapaval
- Faculty of Science and TechnologyNorwegian University of Life SciencesÅsNorway
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Dzurendova S, Olsen PM, Byrtusová D, Tafintseva V, Shapaval V, Horn SJ, Kohler A, Szotkowski M, Marova I, Zimmermann B. Raman spectroscopy online monitoring of biomass production, intracellular metabolites and carbon substrates during submerged fermentation of oleaginous and carotenogenic microorganisms. Microb Cell Fact 2023; 22:261. [PMID: 38110983 PMCID: PMC10729511 DOI: 10.1186/s12934-023-02268-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/10/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Monitoring and control of both growth media and microbial biomass is extremely important for the development of economical bioprocesses. Unfortunately, process monitoring is still dependent on a limited number of standard parameters (pH, temperature, gasses etc.), while the critical process parameters, such as biomass, product and substrate concentrations, are rarely assessable in-line. Bioprocess optimization and monitoring will greatly benefit from advanced spectroscopy-based sensors that enable real-time monitoring and control. Here, Fourier transform (FT) Raman spectroscopy measurement via flow cell in a recirculatory loop, in combination with predictive data modeling, was assessed as a fast, low-cost, and highly sensitive process analytical technology (PAT) system for online monitoring of critical process parameters. To show the general applicability of the method, submerged fermentation was monitored using two different oleaginous and carotenogenic microorganisms grown on two different carbon substrates: glucose fermentation by yeast Rhodotorula toruloides and glycerol fermentation by marine thraustochytrid Schizochytrium sp. Additionally, the online FT-Raman spectroscopy approach was compared with two at-line spectroscopic methods, namely FT-Raman and FT-infrared spectroscopies in high throughput screening (HTS) setups. RESULTS The system can provide real-time concentration data on carbon substrate (glucose and glycerol) utilization, and production of biomass, carotenoid pigments, and lipids (triglycerides and free fatty acids). Robust multivariate regression models were developed and showed high level of correlation between the online FT-Raman spectral data and reference measurements, with coefficients of determination (R2) in the 0.94-0.99 and 0.89-0.99 range for all concentration parameters of Rhodotorula and Schizochytrium fermentation, respectively. The online FT-Raman spectroscopy approach was superior to the at-line methods since the obtained information was more comprehensive, timely and provided more precise concentration profiles. CONCLUSIONS The FT-Raman spectroscopy system with a flow measurement cell in a recirculatory loop, in combination with prediction models, can simultaneously provide real-time concentration data on carbon substrate utilization, and production of biomass, carotenoid pigments, and lipids. This data enables monitoring of dynamic behaviour of oleaginous and carotenogenic microorganisms, and thus can provide critical process parameters for process optimization and control. Overall, this study demonstrated the feasibility of using FT-Raman spectroscopy for online monitoring of fermentation processes.
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Affiliation(s)
- Simona Dzurendova
- Faculty of Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, P.O. Box 5003, 1432, Ås, Norway
| | - Pernille Margrethe Olsen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - Dana Byrtusová
- Faculty of Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, P.O. Box 5003, 1432, Ås, Norway
| | - Valeria Tafintseva
- Faculty of Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, P.O. Box 5003, 1432, Ås, Norway
| | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, P.O. Box 5003, 1432, Ås, Norway
| | - Svein Jarle Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, P.O. Box 5003, 1432, Ås, Norway
| | - Martin Szotkowski
- Institute of Food Science and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkyňova 464/118, Brno, 61200, Czech Republic
| | - Ivana Marova
- Institute of Food Science and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkyňova 464/118, Brno, 61200, Czech Republic
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, P.O. Box 5003, 1432, Ås, Norway.
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Aledda M, Kohler A, Zimmermann B, Patel N, Shapaval V, Tafintseva V. Sparse wavelengths data in mid-infrared spectroscopy: Modelling approaches and channel sampling. J Biophotonics 2023; 16:e202300049. [PMID: 37439117 DOI: 10.1002/jbio.202300049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/31/2023] [Accepted: 07/11/2023] [Indexed: 07/14/2023]
Abstract
Infrared instruments with smaller and cost-effective components such as bandpass filters, single channel detectors, and laser-based light sources are being developed to provide cheaper and faster analysis of biological samples. Such instruments often provide measurements in form of sparse data, which include a collection of single-frequency channels or a collection of channels covering very narrow spectral ranges, called here multi-frequency channels. To keep costs low, the number of channels needs to be kept at a minimum. However, modelling and preprocessing of sparse data needs enough channels to perform the task. The aim of this study therefore was to understand the effect of channels sampling on data modelling results and find optimal modelling algorithm for different type of sparse data. The sparse data was simulated using Fourier Transform Infrared spectra of milk and fungi. Regression models were established to predict fatty acid composition by partial least squares regression (PLSR), multiple linear regression (MLR) and random forest (RF) methods. We observe that PLSR algorithm is very well suited for sparse data such as multi-frequency channels: excellent calibration models were obtained with only three channels comprising three wavenumbers each. The results were comparable to results obtained with full spectra. MLR and RF in turn provided similarly good results using data with single-frequency channels requiring nine channels in total.
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Affiliation(s)
| | - Achim Kohler
- Norwegian University of Life Sciences, Ås, Norway
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Seddon AWR, Zimmermann B. Comment on "Dying in the Sun: Direct evidence for elevated UV-B radiation at the end-Permian mass extinction". Sci Adv 2023; 9:eadi0570. [PMID: 37624886 PMCID: PMC10456835 DOI: 10.1126/sciadv.adi0570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023]
Abstract
Liu et al. present evidence of increased abundance of UV-B-absorbing compounds in fossilized sporomorphs at the end-Permian mass extinction based on Fourier transform infrared (FTIR) spectroscopy. Their approach assumes that UV-B-absorbing compounds are present in the fossilized sporomorphs spanning the extinction interval and that they can be quantified using FTIR. However, further analysis reveals that the signal that they aim to focus on is weak and poorly resolved against nonrandom background interference most likely associated with water vapor. We also show that the peak detection methods that they use are inappropriate for use on these fossil sporomorphs because their methods select only 3.9% of the spectra at the target waveband of interest. The reconstruction that they present is based on baseline variations in the spectra and cannot be confidently attributed to variations in UV-B-absorbing compounds. "Direct" evidence for UV-B radiation at the end-Permian mass extinction cannot be claimed to have been observed in this record.
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Affiliation(s)
- Alistair W R Seddon
- Department of Biological Sciences and Bjerknes Center for Climate Research, University of Bergen, Bergen, Norway
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6
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Shaikh R, Tafintseva V, Nippolainen E, Virtanen V, Solheim J, Zimmermann B, Saarakkala S, Töyräs J, Kohler A, Afara IO. Characterisation of Cartilage Damage via Fusing Mid-Infrared, Near-Infrared, and Raman Spectroscopic Data. J Pers Med 2023; 13:1036. [PMID: 37511649 PMCID: PMC10381453 DOI: 10.3390/jpm13071036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
Mid-infrared spectroscopy (MIR), near-infrared spectroscopy (NIR), and Raman spectroscopy are all well-established analytical techniques in biomedical applications. Since they provide complementary chemical information, we aimed to determine whether combining them amplifies their strengths and mitigates their weaknesses. This study investigates the feasibility of the fusion of MIR, NIR, and Raman spectroscopic data for characterising articular cartilage integrity. Osteochondral specimens from bovine patellae were subjected to mechanical and enzymatic damage, and then MIR, NIR, and Raman data were acquired from the damaged and control specimens. We assessed the capacity of individual spectroscopic methods to classify the samples into damage or control groups using Partial Least Squares Discriminant Analysis (PLS-DA). Multi-block PLS-DA was carried out to assess the potential of data fusion by combining the dataset by applying two-block (MIR and NIR, MIR and Raman, NIR and Raman) and three-block approaches (MIR, NIR, and Raman). The results of the one-block models show a higher classification accuracy for NIR (93%) and MIR (92%) than for Raman (76%) spectroscopy. In contrast, we observed the highest classification efficiency of 94% and 93% for the two-block (MIR and NIR) and three-block models, respectively. The detailed correlative analysis of the spectral features contributing to the discrimination in the three-block models adds considerably more insight into the molecular origin of cartilage damage.
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Affiliation(s)
- Rubina Shaikh
- Department of Technical Physics, University of Eastern Finland, 70211 Kuopio, Finland
- School of Physics, Clinical and Optometric Sciences, Technological University Dublin, D07 XT95 Dublin, Ireland
| | - Valeria Tafintseva
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Ervin Nippolainen
- Department of Technical Physics, University of Eastern Finland, 70211 Kuopio, Finland
| | - Vesa Virtanen
- Research Unit of Medical Imaging, Physics and Technology, University of Oulu, 90570 Oulu, Finland
| | - Johanne Solheim
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Simo Saarakkala
- Research Unit of Medical Imaging, Physics and Technology, University of Oulu, 90570 Oulu, Finland
- Research Unit of Health Sciences and Technology, University of Oulu, 90220 Oulu, Finland
| | - Juha Töyräs
- Department of Technical Physics, University of Eastern Finland, 70211 Kuopio, Finland
- Science Service Center, Kuopio University Hospital, 70210 Kuopio, Finland
- School of Information Technology and Electrical Engineering, The University of Queensland, Brisban, QLD 4072, Australia
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Isaac O Afara
- Department of Technical Physics, University of Eastern Finland, 70211 Kuopio, Finland
- School of Information Technology and Electrical Engineering, The University of Queensland, Brisban, QLD 4072, Australia
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Rehman HU, Cord-Landwehr S, Shapaval V, Dzurendova S, Kohler A, Moerschbacher BM, Zimmermann B. High-throughput vibrational spectroscopy methods for determination of degree of acetylation for chitin and chitosan. Carbohydr Polym 2023; 302:120428. [PMID: 36604090 DOI: 10.1016/j.carbpol.2022.120428] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/07/2022]
Abstract
The rising demand for chitin and chitosan in chemical, agro-food, and healthcare industries is creating a need for rapid and high-throughput analysis. The physicochemical properties of these biopolymers are greatly dependent on the degree of acetylation (DA). Conventional methods for DA determination, such as LC-MS and 1H NMR, are time-consuming when performed on many samples, and therefore efficient methods are needed. Here, high-throughput microplate-based FTIR and FT-Raman methods were compared with their manual counterparts. Partial least squares regression models were based on 30 samples of chitin and chitosan with reference DA values obtained by LC-MS and 1H NMR, and the models were validated on an independent test set of 16 samples. The overall predictive accuracy of the high-throughput methods was at the same level as the manual methods and the well-established LC-MS and 1H NMR methods. Therefore, high-throughput FTIR and FT-Raman DA determination methods have great potential to serve as fast and economical substitutes for traditional methods.
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Affiliation(s)
- Hafeez Ur Rehman
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway.
| | - Stefan Cord-Landwehr
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, Germany.
| | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway.
| | - Simona Dzurendova
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway.
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway.
| | - Bruno M Moerschbacher
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, Germany.
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway.
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Femenias A, Fomina P, Tafintseva V, Freitag S, Shapaval V, Sulyok M, Zimmermann B, Marín S, Krska R, Kohler A, Mizaikoff B. Optimizing extraction solvents for deoxynivalenol analysis in maize via infrared attenuated total reflection spectroscopy and chemometric methods. Anal Methods 2022; 15:36-47. [PMID: 36448527 DOI: 10.1039/d2ay00995a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Farmers, cereal suppliers and processors demand rapid techniques for the assessment of mould-associated contamination. Deoxynivalenol (DON) is among the most important Fusarium toxins and related to human and animal diseases besides causing significant economic losses. Routine analytical techniques for the analysis of DON are either based on chromatographic or immunoanalytical techniques, which are time-consuming and frequently rely on hazardous consumables. The present study evaluates the feasibility of infrared attenuated total reflection spectroscopy (IR-ATR) for the analysis of maize extracts via different solvents optimized for the determination of DON contamination along the regulatory requirements by the European Union (EU) for unprocessed maize (1750 μg kg-1). Reference analysis was done by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). The studied maize samples were either naturally infected or had been artificially inoculated in the field with Fusarium graminearum, Fusarium culmorum or Fusarium verticillioides. Principal component analysis demonstrated that water and methanol-water (70 : 30% v) were optimum solvents for differentiating DON contamination levels. Supervised partial least squares discriminant analysis resulted in excellent classification accuracies of 86.7% and 90.8% for water and methanol-water extracts, respectively. The IR spectra of samples with fungal infection and high DON contamination had distinct spectral features, which could be related to carbohydrates, proteins and lipid content within the investigated extracts.
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Affiliation(s)
- Antoni Femenias
- Applied Mycology Unit, Food Technology Department, University of Lleida, UTPV-XaRTA, Agrotecnio, Av. Rovira Roure, 191, 25198 Lleida, Spain
| | - Polina Fomina
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Valeria Tafintseva
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Stephan Freitag
- University of Natural Resources and Life Sciences, Vienna, Austria
- Department of Agrobiotechnology, IFA-Tulln, Institute of Bioanalytics and Agro-Metabolomics, Konrad-Lorenz-Strasse 20, 3430 Tulln an der Donau, Austria
| | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Michael Sulyok
- University of Natural Resources and Life Sciences, Vienna, Austria
- Department of Agrobiotechnology, IFA-Tulln, Institute of Bioanalytics and Agro-Metabolomics, Konrad-Lorenz-Strasse 20, 3430 Tulln an der Donau, Austria
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Sonia Marín
- Applied Mycology Unit, Food Technology Department, University of Lleida, UTPV-XaRTA, Agrotecnio, Av. Rovira Roure, 191, 25198 Lleida, Spain
| | - Rudolf Krska
- University of Natural Resources and Life Sciences, Vienna, Austria
- Department of Agrobiotechnology, IFA-Tulln, Institute of Bioanalytics and Agro-Metabolomics, Konrad-Lorenz-Strasse 20, 3430 Tulln an der Donau, Austria
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, University Road, Belfast, BT7 1NN, Northern Ireland, UK
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Boris Mizaikoff
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
- Hahn-Schickard, Sedanstrasse 14, 89077 Ulm, Germany
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Ausilio G, Wikenros C, Sand H, Wabakken P, Eriksen A, Zimmermann B. Environmental and anthropogenic features mediate risk from human hunters and wolves for moose. Ecosphere 2022. [DOI: 10.1002/ecs2.4323] [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: 12/25/2022] Open
Affiliation(s)
- G. Ausilio
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Campus Evenstad Inland Norway University of Applied Sciences Koppang Norway
| | - C. Wikenros
- Grimsö Wildlife Research Station, Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - H. Sand
- Grimsö Wildlife Research Station, Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - P. Wabakken
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Campus Evenstad Inland Norway University of Applied Sciences Koppang Norway
| | - A. Eriksen
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Campus Evenstad Inland Norway University of Applied Sciences Koppang Norway
| | - B. Zimmermann
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Campus Evenstad Inland Norway University of Applied Sciences Koppang Norway
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Virtanen V, Tafintseva V, Shaikh R, Nippolainen E, Haas J, Afara I, Töyräs J, Kröger H, Solheim J, Zimmermann B, Kohler A, Mizaikoff B, Finnilä M, Rieppo L, Saarakkala S. Infrared spectroscopy is suitable for objective assessment of articular cartilage health. Osteoarthritis and Cartilage Open 2022; 4:100250. [DOI: 10.1016/j.ocarto.2022.100250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 02/28/2022] [Indexed: 10/18/2022] Open
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Rehman HU, Tafintseva V, Zimmermann B, Solheim JH, Virtanen V, Shaikh R, Nippolainen E, Afara I, Saarakkala S, Rieppo L, Krebs P, Fomina P, Mizaikoff B, Kohler A. Preclassification of Broadband and Sparse Infrared Data by Multiplicative Signal Correction Approach. Molecules 2022; 27:2298. [PMID: 35408697 PMCID: PMC9000438 DOI: 10.3390/molecules27072298] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 02/04/2023] Open
Abstract
Preclassification of raw infrared spectra has often been neglected in scientific literature. Separating spectra of low spectral quality, due to low signal-to-noise ratio, presence of artifacts, and low analyte presence, is crucial for accurate model development. Furthermore, it is very important for sparse data, where it becomes challenging to visually inspect spectra of different natures. Hence, a preclassification approach to separate infrared spectra for sparse data is needed. In this study, we propose a preclassification approach based on Multiplicative Signal Correction (MSC). The MSC approach was applied on human and the bovine knee cartilage broadband Fourier Transform Infrared (FTIR) spectra and on a sparse data subset comprising of only seven wavelengths. The goal of the preclassification was to separate spectra with analyte-rich signals (i.e., cartilage) from spectra with analyte-poor (and high-matrix) signals (i.e., water). The human datasets 1 and 2 contained 814 and 815 spectra, while the bovine dataset contained 396 spectra. A pure water spectrum was used as a reference spectrum in the MSC approach. A threshold for the root mean square error (RMSE) was used to separate cartilage from water spectra for broadband and the sparse spectral data. Additionally, standard noise-to-ratio and principle component analysis were applied on broadband spectra. The fully automated MSC preclassification approach, using water as reference spectrum, performed as well as the manual visual inspection. Moreover, it enabled not only separation of cartilage from water spectra in broadband spectral datasets, but also in sparse datasets where manual visual inspection cannot be applied.
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Affiliation(s)
- Hafeez Ur Rehman
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1430 Ås, Norway; (V.T.); (B.Z.); (J.H.S.); (A.K.)
| | - Valeria Tafintseva
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1430 Ås, Norway; (V.T.); (B.Z.); (J.H.S.); (A.K.)
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1430 Ås, Norway; (V.T.); (B.Z.); (J.H.S.); (A.K.)
| | - Johanne Heitmann Solheim
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1430 Ås, Norway; (V.T.); (B.Z.); (J.H.S.); (A.K.)
| | - Vesa Virtanen
- Research Unit of Medical Imaging, Physics and Technology, Faculty of Medicine, University of Oulu, 90570 Oulu, Finland; (V.V.); (S.S.); (L.R.)
| | - Rubina Shaikh
- Department of Applied Physics, University of Eastern Finland, 70210 Kuopio, Finland; (R.S.); (E.N.); (I.A.)
- Department of Orthopedics, Traumatology, Hand Surgery, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Ervin Nippolainen
- Department of Applied Physics, University of Eastern Finland, 70210 Kuopio, Finland; (R.S.); (E.N.); (I.A.)
| | - Isaac Afara
- Department of Applied Physics, University of Eastern Finland, 70210 Kuopio, Finland; (R.S.); (E.N.); (I.A.)
| | - Simo Saarakkala
- Research Unit of Medical Imaging, Physics and Technology, Faculty of Medicine, University of Oulu, 90570 Oulu, Finland; (V.V.); (S.S.); (L.R.)
| | - Lassi Rieppo
- Research Unit of Medical Imaging, Physics and Technology, Faculty of Medicine, University of Oulu, 90570 Oulu, Finland; (V.V.); (S.S.); (L.R.)
| | - Patrick Krebs
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, 89081 Ulm, Germany; (P.K.); (P.F.); (B.M.)
| | - Polina Fomina
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, 89081 Ulm, Germany; (P.K.); (P.F.); (B.M.)
| | - Boris Mizaikoff
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, 89081 Ulm, Germany; (P.K.); (P.F.); (B.M.)
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1430 Ås, Norway; (V.T.); (B.Z.); (J.H.S.); (A.K.)
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12
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Solheim JH, Zimmermann B, Tafintseva V, Dzurendová S, Shapaval V, Kohler A. The Use of Constituent Spectra and Weighting in Extended Multiplicative Signal Correction in Infrared Spectroscopy. Molecules 2022; 27:molecules27061900. [PMID: 35335264 PMCID: PMC8948808 DOI: 10.3390/molecules27061900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/09/2022] [Accepted: 03/12/2022] [Indexed: 11/30/2022]
Abstract
Extended multiplicative signal correction (EMSC) is a widely used preprocessing technique in infrared spectroscopy. EMSC is a model-based method favored for its flexibility and versatility. The model can be extended by adding constituent spectra to explicitly model-known analytes or interferents. This paper addresses the use of constituent spectra and demonstrates common pitfalls. It clarifies the difference between analyte and interferent spectra, and the importance of orthogonality between model spectra. Different normalization approaches are discussed, and the importance of weighting in the EMSC is demonstrated. The paper illustrates how constituent analyte spectra can be estimated, and how they can be used to extract additional information from spectral features. It is shown that the EMSC parameters can be used in both regression tasks and segmentation tasks.
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13
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Virtanen V, Nippolainen E, Shaikh R, Afara IO, Töyräs J, Solheim J, Tafintseva V, Zimmermann B, Kohler A, Saarakkala S, Rieppo L. Infrared Fiber-Optic Spectroscopy Detects Bovine Articular Cartilage Degeneration. Cartilage 2021; 13:285S-294S. [PMID: 33615831 PMCID: PMC8804829 DOI: 10.1177/1947603521993221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVE Joint injuries may lead to degeneration of cartilage tissue and initiate development of posttraumatic osteoarthritis. Arthroscopic surgeries can be used to treat joint injuries, but arthroscopic evaluation of articular cartilage quality is subjective. Fourier transform infrared spectroscopy combined with fiber optics and attenuated total reflectance crystal could be used for the assessment of tissue quality during arthroscopy. We hypothesize that fiber-optic mid-infrared spectroscopy can detect enzymatically and mechanically induced damage similar to changes occurring during progression of osteoarthritis. DESIGN Bovine patellar cartilage plugs were extracted and degraded enzymatically and mechanically. Adjacent untreated samples were utilized as controls. Enzymatic degradation was done using collagenase and trypsin enzymes. Mechanical damage was induced by (1) dropping a weight impactor on the cartilage plugs and (2) abrading the cartilage surface with a rotating sandpaper. Fiber-optic mid-infrared spectroscopic measurements were conducted before and after treatments, and spectral changes were assessed with random forest, partial least squares discriminant analysis, and support vector machine classifiers. RESULTS All models had excellent classification performance for detecting the different enzymatic and mechanical damage on cartilage matrix. Random forest models achieved accuracies between 90.3% and 77.8%, while partial least squares model accuracies ranged from 95.8% to 84.7%, and support vector machine accuracies from 91.7% to 80.6%. CONCLUSIONS The results suggest that fiber-optic Fourier transform infrared spectroscopy attenuated total reflectance spectroscopy is a viable way to detect minor and major degeneration of articular cartilage. Objective measures provided by fiber-optic spectroscopic methods could improve arthroscopic evaluation of cartilage damage.
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Affiliation(s)
- Vesa Virtanen
- Research Unit of Medical Imaging,
Physics and Technology, Faculty of Medicine, University of Oulu, Oulu, Finland,Vesa Virtanen, Research Unit of Medical
Imaging, Physics and Technology, Faculty of Medicine, University of Oulu,
Aapistie 5 A, Oulu, Pohjois-Pohjanmaa 90220, Finland.
| | - Ervin Nippolainen
- Department of Applied Physics,
University of Eastern Finland, Kuopio, Finland
| | - Rubina Shaikh
- Department of Applied Physics,
University of Eastern Finland, Kuopio, Finland
| | - Isaac O. Afara
- Department of Applied Physics,
University of Eastern Finland, Kuopio, Finland,School of Information Technology and
Electrical Engineering, The University of Queensland, Brisbane, Queensland,
Australia
| | - Juha Töyräs
- Department of Applied Physics,
University of Eastern Finland, Kuopio, Finland,Diagnostic Imaging Center, Kuopio
University Hospital, Kuopio, Finland,School of Information Technology and
Electrical Engineering, The University of Queensland, Brisbane, Queensland,
Australia
| | - Johanne Solheim
- Biospectroscopy and Data Modeling Group,
Faculty of Science and Technology, Norwegian University of Life Sciences, Ås,
Norway
| | - Valeria Tafintseva
- Biospectroscopy and Data Modeling Group,
Faculty of Science and Technology, Norwegian University of Life Sciences, Ås,
Norway
| | - Boris Zimmermann
- Biospectroscopy and Data Modeling Group,
Faculty of Science and Technology, Norwegian University of Life Sciences, Ås,
Norway
| | - Achim Kohler
- Biospectroscopy and Data Modeling Group,
Faculty of Science and Technology, Norwegian University of Life Sciences, Ås,
Norway
| | - Simo Saarakkala
- Research Unit of Medical Imaging,
Physics and Technology, Faculty of Medicine, University of Oulu, Oulu, Finland,Department of Diagnostic Radiology, Oulu
University Hospital, Oulu, Finland
| | - Lassi Rieppo
- Research Unit of Medical Imaging,
Physics and Technology, Faculty of Medicine, University of Oulu, Oulu, Finland
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14
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Solheim JH, Borondics F, Zimmermann B, Sandt C, Muthreich F, Kohler A. An automated approach for fringe frequency estimation and removal in infrared spectroscopy and hyperspectral imaging of biological samples. J Biophotonics 2021; 14:e202100148. [PMID: 34468082 DOI: 10.1002/jbio.202100148] [Citation(s) in RCA: 2] [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: 05/05/2021] [Revised: 08/23/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
In infrared spectroscopy of thin film samples, interference introduces distortions in spectra, commonly referred to as fringes. Fringes may alter absorbance peak ratios, which hampers the spectral analysis. We have previously introduced extended multiplicative signal correction (EMSC) for fringes correction. In the current article, we provide a robust open-source algorithm for fringe correction in infrared spectroscopy and propose several improvements to the Fringe EMSC model. The suggested algorithm achieves a more precise fringe frequency estimation by mean centering of the measured spectrum and applying a window function prior to the Fourier transform. It selects two frequencies from a user defined number of maxima in the Fourier domain. The improved Fringe EMSC algorithm is validated on two experimental datasets, one of them being a hyperspectral image. Techniques for separating sample spectra from background spectra in hyperspectral images, and techniques to identify spectra affected by fringes are also provided.
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Affiliation(s)
- Johanne Heitmann Solheim
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin-BP48, Gif-sur-Yvette CEDEX, France
| | - Ferenc Borondics
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin-BP48, Gif-sur-Yvette CEDEX, France
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Christophe Sandt
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin-BP48, Gif-sur-Yvette CEDEX, France
| | - Florian Muthreich
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
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15
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Tan A, Lai G, Saw S, Chua K, Takano A, Ong B, Koh T, Jain A, Tan W, Ng Q, Kanesvaran R, Rajasekaran T, Kalshnikova E, Shchegrova S, H. -Ta, Lin J, Renner D, Sethi H, Zimmermann B, Aleshin A, Lim W, Tan E, Skanderup A, Ang M, Tan D. MA07.06 Circulating Tumor DNA for Monitoring Minimal Residual Disease and Early Detection of Recurrence in Early Stage Lung Cancer. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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16
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Klarin D, Kalashnikova E, Wu HT, Mehta S, Salari R, Sethi H, Zimmermann B, Billings P, Aleshin A. 1762P Association of clonal hematopoiesis of indeterminate potential with higher risk of disease progression. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.1707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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17
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Dzurendová S, Shapaval V, Tafintseva V, Kohler A, Byrtusová D, Szotkowski M, Márová I, Zimmermann B. Assessment of Biotechnologically Important Filamentous Fungal Biomass by Fourier Transform Raman Spectroscopy. Int J Mol Sci 2021; 22:6710. [PMID: 34201486 PMCID: PMC8269384 DOI: 10.3390/ijms22136710] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 05/19/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 12/11/2022] Open
Abstract
Oleaginous filamentous fungi can accumulate large amount of cellular lipids and biopolymers and pigments and potentially serve as a major source of biochemicals for food, feed, chemical, pharmaceutical, and transport industries. We assessed suitability of Fourier transform (FT) Raman spectroscopy for screening and process monitoring of filamentous fungi in biotechnology. Six Mucoromycota strains were cultivated in microbioreactors under six growth conditions (three phosphate concentrations in the presence and absence of calcium). FT-Raman and FT-infrared (FTIR) spectroscopic data was assessed in respect to reference analyses of lipids, phosphorus, and carotenoids by using principal component analysis (PCA), multiblock or consensus PCA, partial least square regression (PLSR), and analysis of spectral variation due to different design factors by an ANOVA model. All main chemical biomass constituents were detected by FT-Raman spectroscopy, including lipids, proteins, cell wall carbohydrates, and polyphosphates, and carotenoids. FT-Raman spectra clearly show the effect of growth conditions on fungal biomass. PLSR models with high coefficients of determination (0.83-0.94) and low error (approximately 8%) for quantitative determination of total lipids, phosphates, and carotenoids were established. FT-Raman spectroscopy showed great potential for chemical analysis of biomass of oleaginous filamentous fungi. The study demonstrates that FT-Raman and FTIR spectroscopies provide complementary information on main fungal biomass constituents.
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Affiliation(s)
- Simona Dzurendová
- Faculty of Science and Technology, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway; (S.D.); (V.S.); (V.T.); (A.K.); (D.B.)
| | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway; (S.D.); (V.S.); (V.T.); (A.K.); (D.B.)
| | - Valeria Tafintseva
- Faculty of Science and Technology, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway; (S.D.); (V.S.); (V.T.); (A.K.); (D.B.)
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway; (S.D.); (V.S.); (V.T.); (A.K.); (D.B.)
| | - Dana Byrtusová
- Faculty of Science and Technology, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway; (S.D.); (V.S.); (V.T.); (A.K.); (D.B.)
- Faculty of Chemistry, Brno University of Technology, Purkyňova 464/118, 61200 Brno, Czech Republic; (M.S.); (I.M.)
| | - Martin Szotkowski
- Faculty of Chemistry, Brno University of Technology, Purkyňova 464/118, 61200 Brno, Czech Republic; (M.S.); (I.M.)
| | - Ivana Márová
- Faculty of Chemistry, Brno University of Technology, Purkyňova 464/118, 61200 Brno, Czech Republic; (M.S.); (I.M.)
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway; (S.D.); (V.S.); (V.T.); (A.K.); (D.B.)
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18
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Dzurendova S, Zimmermann B, Kohler A, Reitzel K, Nielsen UG, Dupuy--Galet BX, Leivers S, Horn SJ, Shapaval V. Calcium Affects Polyphosphate and Lipid Accumulation in Mucoromycota Fungi. J Fungi (Basel) 2021; 7:jof7040300. [PMID: 33920847 PMCID: PMC8071181 DOI: 10.3390/jof7040300] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/08/2021] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
Calcium controls important processes in fungal metabolism, such as hyphae growth, cell wall synthesis, and stress tolerance. Recently, it was reported that calcium affects polyphosphate and lipid accumulation in fungi. The purpose of this study was to assess the effect of calcium on the accumulation of lipids and polyphosphate for six oleaginous Mucoromycota fungi grown under different phosphorus/pH conditions. A Duetz microtiter plate system (Duetz MTPS) was used for the cultivation. The compositional profile of the microbial biomass was recorded using Fourier-transform infrared spectroscopy, the high throughput screening extension (FTIR-HTS). Lipid content and fatty acid profiles were determined using gas chromatography (GC). Cellular phosphorus was determined using assay-based UV-Vis spectroscopy, and accumulated phosphates were characterized using solid-state 31P nuclear magnetic resonance spectroscopy. Glucose consumption was estimated by FTIR-attenuated total reflection (FTIR-ATR). Overall, the data indicated that calcium availability enhances polyphosphate accumulation in Mucoromycota fungi, while calcium deficiency increases lipid production, especially under acidic conditions (pH 2-3) caused by the phosphorus limitation. In addition, it was observed that under acidic conditions, calcium deficiency leads to increase in carotenoid production. It can be concluded that calcium availability can be used as an optimization parameter in fungal fermentation processes to enhance the production of lipids or polyphosphates.
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Affiliation(s)
- Simona Dzurendova
- Faculty of Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, 1433 Ås, Norway; (B.Z.); (A.K.); (B.X.D.--G.); (V.S.)
- Correspondence: or
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, 1433 Ås, Norway; (B.Z.); (A.K.); (B.X.D.--G.); (V.S.)
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, 1433 Ås, Norway; (B.Z.); (A.K.); (B.X.D.--G.); (V.S.)
| | - Kasper Reitzel
- Department of Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark;
| | - Ulla Gro Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark;
| | - Benjamin Xavier Dupuy--Galet
- Faculty of Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, 1433 Ås, Norway; (B.Z.); (A.K.); (B.X.D.--G.); (V.S.)
| | - Shaun Leivers
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Christian Magnus Falsens vei 1, 1433 Ås, Norway; (S.L.); (S.J.H.)
| | - Svein Jarle Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Christian Magnus Falsens vei 1, 1433 Ås, Norway; (S.L.); (S.J.H.)
| | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, 1433 Ås, Norway; (B.Z.); (A.K.); (B.X.D.--G.); (V.S.)
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19
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Langseter AM, Dzurendova S, Shapaval V, Kohler A, Ekeberg D, Zimmermann B. Evaluation and optimisation of direct transesterification methods for the assessment of lipid accumulation in oleaginous filamentous fungi. Microb Cell Fact 2021; 20:59. [PMID: 33658027 PMCID: PMC7931520 DOI: 10.1186/s12934-021-01542-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 11/05/2020] [Accepted: 02/15/2021] [Indexed: 12/18/2022] Open
Abstract
Background Oleaginous filamentous fungi can accumulate large amount of cellular lipids and potentially serve as a major source of oleochemicals for food, feed, chemical, pharmaceutical, and transport industries. Transesterification of microbial oils is an essential step in microbial lipid production at both laboratory and industrial scale. Direct transesterification can considerably reduce costs, increase sample throughput and improve lipid yields (in particular fatty acid methyl esters, FAMEs). There is a need for the assessment of the direct transesterification methods on a biomass of filamentous fungi due to their unique properties, specifically resilient cell wall and wide range of lipid content and composition. In this study we have evaluated and optimised three common direct transesterification methods and assessed their suitability for processing of fungal biomass. Results The methods, based on hydrochloric acid (Lewis method), sulphuric acid (Wahlen method), and acetyl chloride (Lepage method), were evaluated on six different strains of Mucoromycota fungi by using different internal standards for gas chromatography measurements. Moreover, Fourier transform infrared (FTIR) spectroscopy was used for the detection of residual lipids in the biomass after the transesterification reaction/extraction, while transesterification efficiency was evaluated by nuclear magnetic resonance spectroscopy. The results show that the majority of lipids, in particular triglycerides, were extracted for all methods, though several methods had substandard transesterification yields. Lewis method, optimised with respect to solvent to co-solvent ratio and reaction time, as well as Lepage method, offer precise estimate of FAME-based lipids in fungal biomass. Conclusions The results show that Lepage and Lewis methods are suitable for lipid analysis of oleaginous filamentous fungi. The significant difference in lipid yields results, obtained by optimised and standard Lewis methods, indicates that some of the previously reported lipid yields for oleaginous filamentous fungi must be corrected upwards. The study demonstrates value of biomass monitoring by FTIR, importance of optimal solvent to co-solvent ratio, as well as careful selection and implementation of internal standards for gas chromatography.
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Affiliation(s)
- Anne Marie Langseter
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway
| | - Simona Dzurendova
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway
| | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway
| | - Dag Ekeberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway.
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20
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Slaný O, Klempová T, Shapaval V, Zimmermann B, Kohler A, Čertík M. Animal Fat as a Substrate for Production of n-6 Fatty Acids by Fungal Solid-State Fermentation. Microorganisms 2021; 9:170. [PMID: 33466747 PMCID: PMC7830168 DOI: 10.3390/microorganisms9010170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 12/03/2022] Open
Abstract
The method of solid-state fermentation (SSF) represents a powerful technology for the fortification of animal-based by-products. Oleaginous Zygomycetes fungi are efficient microbial cell factories used in SSF to valorize a wide range of waste and rest cereal materials. The application of this fermentation technique for utilization and biotransformation of animal-based materials represents a distinguished step in their treatment. In this study, for the first time, the strain Umbelopsis isabellina CCF2412 was used for the bioconversion of animal fat by-products to the fermented bioproducts enriched with n-6 polyunsaturated fatty acids, mainly γ-linolenic acid (GLA). Bioconversion of both cereals and the animal fat by-product resulted in the production of fermented bioproducts enriched with not just GLA (maximal yield was 6.4 mg GLA/g of fermented bioproduct), but also with high yields of glucosamine. Moreover, the fermentation on the cornmeal matrix led to obtaining bioproduct enriched with β-carotene. An increased amount of β-carotene content improved the antioxidant stability of obtained fermented bioproducts. Furthermore, the application of Fourier-transform infrared spectroscopy for rapid analysis and characterization of the biochemical profile of obtained SSF bioproducts was also studied.
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Affiliation(s)
- Ondrej Slaný
- Faculty of Chemical and Food Technology, Institute of Biotechnology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (T.K.); (M.Č.)
| | - Tatiana Klempová
- Faculty of Chemical and Food Technology, Institute of Biotechnology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (T.K.); (M.Č.)
| | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432 Ås, Norway; (V.S.); (B.Z.); (A.K.)
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432 Ås, Norway; (V.S.); (B.Z.); (A.K.)
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432 Ås, Norway; (V.S.); (B.Z.); (A.K.)
| | - Milan Čertík
- Faculty of Chemical and Food Technology, Institute of Biotechnology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (T.K.); (M.Č.)
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21
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Ococks E, Ng A, Devonshire G, Dashner S, Chan WC, Sharma S, Wu HT, Redmond A, Northrop A, Grehan N, Sethi H, Zimmermann B, Smyth E, Aleshin A, Fitzgerald R. 370P Bespoke circulating tumour DNA assay for the detection of minimal residual disease in esophageal adenocarcinoma patients. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.10.594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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22
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Henriksen T, Tarazona N, Reinert T, Carbonell-Asins J, Roda D, Huerta M, Roselló S, Madsen A, Iversen L, Gotschalck K, Sharma S, Wu HT, Shchegrova S, Tin A, Sethi H, Zimmermann B, Aleshin A, Andersen C, Cervantes A. 420P Minimal residual disease detection and tracking tumour evolution using ctDNA in stage I-III colorectal cancer patients. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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23
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Dzurendova S, Zimmermann B, Tafintseva V, Kohler A, Ekeberg D, Shapaval V. The influence of phosphorus source and the nature of nitrogen substrate on the biomass production and lipid accumulation in oleaginous Mucoromycota fungi. Appl Microbiol Biotechnol 2020; 104:8065-8076. [PMID: 32789746 PMCID: PMC7447667 DOI: 10.1007/s00253-020-10821-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 05/22/2020] [Revised: 07/28/2020] [Accepted: 08/05/2020] [Indexed: 12/26/2022]
Abstract
Abstract Oleaginous filamentous fungi grown under the nitrogen limitation, accumulate high amounts of lipids in the form of triacylglycerides (TAGs) with fatty acid profiles similar to plant and fish oils. In this study, we investigate the effect of six phosphorus source concentrations combined with two types of nitrogen substrate (yeast extract and ammonium sulphate), on the biomass formation, lipid production, and fatty acid profile for nine oleaginous Mucoromycota fungi. The analysis of fatty acid profiles was performed by gas chromatography with flame ionization detector (GC-FID) and the lipid yield was estimated gravimetrically. Yeast extract could be used as both nitrogen and phosphorus source, without additional inorganic phosphorus supplementation. The use of inorganic nitrogen source (ammonium sulphate) requires strain-specific optimization of phosphorus source amount to obtain optimal lipid production regarding quantity and fatty acid profiles. Lipid production was decreased in ammonium sulphate-based media when phosphorus source was limited in all strains except for Rhizopus stolonifer. High phosphorus source concentration inhibited the growth of Mortierella fungi. The biomass (22 g/L) and lipid (14 g/L) yield of Umbelopsis vinacea was the highest among all the tested strains. Key points • The strain specific P requirements of Mucoromycota depend on the nature of N source. • Yeast extract leads to consistent biomass and lipid yield and fatty acids profiles. • Umbelopsis vinacea showed the highest biomass (22 g/L) and lipid (14 g/L) yield. • High P source amounts inhibit the growth of Mortierella fungi. Electronic supplementary material The online version of this article (10.1007/s00253-020-10821-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simona Dzurendova
- Faculty of Science and Technology, Norwegian University of Life Sciences, Droebakveien 31, 1430, Aas, Norway.
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Droebakveien 31, 1430, Aas, Norway
| | - Valeria Tafintseva
- Faculty of Science and Technology, Norwegian University of Life Sciences, Droebakveien 31, 1430, Aas, Norway
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Droebakveien 31, 1430, Aas, Norway
| | - Dag Ekeberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Christian Magnus Falsens vei 1, 1433, Aas, Norway
| | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, Droebakveien 31, 1430, Aas, Norway
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Dzurendova S, Zimmermann B, Kohler A, Tafintseva V, Slany O, Certik M, Shapaval V. Microcultivation and FTIR spectroscopy-based screening revealed a nutrient-induced co-production of high-value metabolites in oleaginous Mucoromycota fungi. PLoS One 2020; 15:e0234870. [PMID: 32569317 PMCID: PMC7307774 DOI: 10.1371/journal.pone.0234870] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 03/06/2020] [Accepted: 06/03/2020] [Indexed: 12/22/2022] Open
Abstract
Mucoromycota fungi possess a versatile metabolism and can utilize various substrates for production of industrially important products, such as lipids, chitin/chitosan, polyphosphates, pigments, alcohols and organic acids. However, as far as commercialisation is concerned, establishing industrial biotechnological processes based on Mucoromycota fungi is still challenging due to the high production costs compared to the final product value. Therefore, the development of co-production concept is highly desired since more than one valuable product could be produced at the time and the process has a potentially higher viability. To develop such biotechnological strategy, we applied a high throughput approach consisting of micro-titre cultivation and FTIR spectroscopy. This approach allows single-step biochemical fingerprinting of either fungal biomass or growth media without tedious extraction of metabolites. The influence of two types of nitrogen sources and different levels of inorganic phosphorus on the co-production of lipids, chitin/chitosan and polyphosphates for nine different oleaginous Mucoromycota fungi was evaluated. FTIR analysis of biochemical composition of Mucoromycota fungi and biomass yield showed that variation in inorganic phosphorus had higher effect when inorganic nitrogen source-ammonium sulphate-was used. It was observed that: (1) Umbelopsis vinacea reached almost double biomass yield compared to other strains when yeast extract was used as nitrogen source while phosphorus limitation had little effect on the biomass yield; (2) Mucor circinelloides, Rhizopus stolonifer, Amylomyces rouxii, Absidia glauca and Lichtheimia corymbifera overproduced chitin/chitosan under the low pH caused by the limitation of inorganic phosphorus; (3) Mucor circinelloides, Amylomyces rouxii, Rhizopus stolonifer and Absidia glauca were able to store polyphosphates in addition to lipids when high concentration of inorganic phosphorus was used; (4) the biomass and lipid yield of high-value lipid producers Mortierella alpina and Mortierella hyalina were significantly increased when high concentrations of inorganic phosphorus were combined with ammonium sulphate, while the same amount of inorganic phosphorus combined with yeast extract showed negative impact on the growth and lipid accumulation. FTIR spectroscopy revealed the co-production potential of several oleaginous Mucoromycota fungi forming lipids, chitin/chitosan and polyphosphates in a single cultivation process.
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Affiliation(s)
- Simona Dzurendova
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
- * E-mail: ,
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Valeria Tafintseva
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Ondrej Slany
- Faculty of Chemical and Food Technology, Slovak Technical University, Bratislava, Slovakia
| | - Milan Certik
- Faculty of Chemical and Food Technology, Slovak Technical University, Bratislava, Slovakia
| | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
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Diehn S, Zimmermann B, Tafintseva V, Bağcıoğlu M, Kohler A, Ohlson M, Fjellheim S, Kneipp J. Discrimination of grass pollen of different species by FTIR spectroscopy of individual pollen grains. Anal Bioanal Chem 2020; 412:6459-6474. [PMID: 32350580 PMCID: PMC7442581 DOI: 10.1007/s00216-020-02628-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/11/2020] [Accepted: 03/28/2020] [Indexed: 02/06/2023]
Abstract
Fourier-transform infrared (FTIR) spectroscopy enables the chemical characterization and identification of pollen samples, leading to a wide range of applications, such as paleoecology and allergology. This is of particular interest in the identification of grass (Poaceae) species since they have pollen grains of very similar morphology. Unfortunately, the correct identification of FTIR microspectroscopy spectra of single pollen grains is hindered by strong spectral contributions from Mie scattering. Embedding of pollen samples in paraffin helps to retrieve infrared spectra without scattering artifacts. In this study, pollen samples from 10 different populations of five grass species (Anthoxanthum odoratum, Bromus inermis, Hordeum bulbosum, Lolium perenne, and Poa alpina) were embedded in paraffin, and their single grain spectra were obtained by FTIR microspectroscopy. Spectra were subjected to different preprocessing in order to suppress paraffin influence on spectral classification. It is shown that decomposition by non-negative matrix factorization (NMF) and extended multiplicative signal correction (EMSC) that utilizes a paraffin constituent spectrum, respectively, leads to good success rates for the classification of spectra with respect to species by a partial least square discriminant analysis (PLS-DA) model in full cross-validation for several species. PLS-DA, artificial neural network, and random forest classifiers were applied on the EMSC-corrected spectra using an independent validation to assign spectra from unknown populations to the species. Variation within and between species, together with the differences in classification results, is in agreement with the systematics within the Poaceae family. The results illustrate the great potential of FTIR microspectroscopy for automated classification and identification of grass pollen, possibly together with other, complementary methods for single pollen chemical characterization.
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Affiliation(s)
- Sabrina Diehn
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Valeria Tafintseva
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Murat Bağcıoğlu
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Mikael Ohlson
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Siri Fjellheim
- Faculty of Biosciences, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Janina Kneipp
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany.
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Kenđel A, Zimmermann B. Chemical Analysis of Pollen by FT-Raman and FTIR Spectroscopies. Front Plant Sci 2020; 11:352. [PMID: 32296453 PMCID: PMC7136416 DOI: 10.3389/fpls.2020.00352] [Citation(s) in RCA: 25] [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] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/10/2020] [Indexed: 05/13/2023]
Abstract
Pollen studies are important for the assessment of present and past environment, including biodiversity, sexual reproduction of plants and plant-pollinator interactions, monitoring of aeroallergens, and impact of climate and pollution on wild communities and cultivated crops. Although information on chemical composition of pollen is of importance in all of those research areas, pollen chemistry has been rarely measured due to complex and time-consuming analyses. Vibrational spectroscopies, coupled with multivariate data analysis, have shown great potential for rapid chemical characterization, identification and classification of pollen. This study, comprising 219 species from all principal taxa of seed plants, has demonstrated that high-quality Raman spectra of pollen can be obtained by Fourier transform (FT) Raman spectroscopy. In combination with Fourier transform infrared spectroscopy (FTIR), FT-Raman spectroscopy is obtaining comprehensive information on pollen chemistry. Presence of all the main biochemical constituents of pollen, such as proteins, lipids, carbohydrates, carotenoids and sporopollenins, have been identified and detected in the spectra, and the study shows approaches to measure relative and absolute content of these constituents. The results show that FT-Raman spectroscopy has clear advantage over standard dispersive Raman measurements, in particular for measurement of pollen samples with high pigment content. FT-Raman spectra are strongly biased toward chemical composition of pollen wall constituents, namely sporopollenins and pigments. This makes Raman spectra complementary to FTIR spectra, which over-represent chemical constituents of the grain interior, such as lipids and carbohydrates. The results show a large variability in pollen chemistry for families, genera and even congeneric species, revealing wide range of reproductive strategies, from storage of nutrients to variation in carotenoids and phenylpropanoids. The information on pollen's chemical patterns for major plant taxa should be of outstanding value for various studies in plant biology and ecology, including aerobiology, palaeoecology, forensics, community ecology, plant-pollinator interactions, and climate effects on plants.
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Affiliation(s)
- Adriana Kenđel
- Division of Analytical Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
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Blomqvist J, Langseter A, Markina D, Zimmermann B, Kohler A, Shapaval V. Production of polyunsaturated fatty acids from animal fat emulsion by oleaginous filamentous fungi. J Biotechnol 2019. [DOI: 10.1016/j.jbiotec.2019.05.065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Langster A, Zimmermann B, Kohler A, Blomqvist J, Sandgren M, Passoth V, Marova I, Shapaval V. Green solvent extraction of microbial lipids. J Biotechnol 2019. [DOI: 10.1016/j.jbiotec.2019.05.066] [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: 11/15/2022]
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Aab A, Abreu P, Aglietta M, Albuquerque I, Albury J, Allekotte I, Almela A, Alvarez Castillo J, Alvarez-Muñiz J, Anastasi G, Anchordoqui L, Andrada B, Andringa S, Aramo C, Asorey H, Assis P, Avila G, Badescu A, Bakalova A, Balaceanu A, Barbato F, Barreira Luz R, Baur S, Becker K, Bellido J, Berat C, Bertaina M, Bertou X, Biermann P, Biteau J, Blaess S, Blanco A, Blazek J, Bleve C, Boháčová M, Boncioli D, Bonifazi C, Borodai N, Botti A, Brack J, Bretz T, Bridgeman A, Briechle F, Buchholz P, Bueno A, Buitink S, Buscemi M, Caballero-Mora K, Caccianiga L, Calcagni L, Cancio A, Canfora F, Carceller J, Caruso R, Castellina A, Catalani F, Cataldi G, Cazon L, Cerda M, Chinellato J, Chudoba J, Chytka L, Clay R, Cobos Cerutti A, Colalillo R, Coleman A, Coluccia M, Conceição R, Condorelli A, Consolati G, Contreras F, Convenga F, Cooper M, Coutu S, Covault C, Daniel B, Dasso S, Daumiller K, Dawson B, Day J, de Almeida R, de Jong S, De Mauro G, de Mello Neto J, De Mitri I, de Oliveira J, de Oliveira Salles F, de Souza V, Debatin J, del Río M, Deligny O, Dhital N, Díaz Castro M, Diogo F, Dobrigkeit C, D’Olivo J, Dorosti Q, dos Anjos R, Dova M, Dundovic A, Ebr J, Engel R, Erdmann M, Escobar C, Etchegoyen A, Falcke H, Farmer J, Farrar G, Fauth A, Fazzini N, Feldbusch F, Fenu F, Ferreyro L, Figueira J, Filipčič A, Freire M, Fujii T, Fuster A, García B, Gemmeke H, Gherghel-Lascu A, Ghia P, Giaccari U, Giammarchi M, Giller M, Głas D, Glombitza J, Gobbi F, Golup G, Gómez Berisso M, Gómez Vitale P, Gongora J, González N, Goos I, Góra D, Gorgi A, Gottowik M, Grubb T, Guarino F, Guedes G, Guido E, Halliday R, Hampel M, Hansen P, Harari D, Harrison T, Harvey V, Haungs A, Hebbeker T, Heck D, Heimann P, Hill G, Hojvat C, Holt E, Homola P, Hörandel J, Horvath P, Hrabovský M, Huege T, Hulsman J, Insolia A, Isar P, Jandt I, Johnsen J, Josebachuili M, Jurysek J, Kääpä A, Kampert K, Keilhauer B, Kemmerich N, Kemp J, Klages H, Kleifges M, Kleinfeller J, Krause R, Kuempel D, Kukec Mezek G, Kuotb Awad A, Lago B, LaHurd D, Lang R, Legumina R, Leigui de Oliveira M, Lenok V, Letessier-Selvon A, Lhenry-Yvon I, Lippmann O, Lo Presti D, Lopes L, López R, López Casado A, Lorek R, Luce Q, Lucero A, Malacari M, Mancarella G, Mandat D, Manning B, Mantsch P, Mariazzi A, Mariş I, Marsella G, Martello D, Martinez H, Martínez Bravo O, Mastrodicasa M, Mathes H, Mathys S, Matthews J, Matthiae G, Mayotte E, Mazur P, Medina-Tanco G, Melo D, Menshikov A, Merenda KD, Michal S, Micheletti M, Middendorf L, Miramonti L, Mitrica B, Mockler D, Mollerach S, Montanet F, Morello C, Morlino G, Mostafá M, Müller A, Muller M, Müller S, Mussa R, Nellen L, Nguyen P, Niculescu-Oglinzanu M, Niechciol M, Nitz D, Nosek D, Novotny V, Nožka L, Nucita A, Núñez L, Olinto A, Palatka M, Pallotta J, Panetta M, Papenbreer P, Parente G, Parra A, Pech M, Pedreira F, Pȩkala J, Pelayo R, Peña-Rodriguez J, Pereira L, Perlin M, Perrone L, Peters C, Petrera S, Phuntsok J, Pierog T, Pimenta M, Pirronello V, Platino M, Poh J, Pont B, Porowski C, Prado R, Privitera P, Prouza M, Puyleart A, Querchfeld S, Quinn S, Ramos-Pollan R, Rautenberg J, Ravignani D, Reininghaus M, Ridky J, Riehn F, Risse M, Ristori P, Rizi V, Rodrigues de Carvalho W, Rodriguez Rojo J, Roncoroni M, Roth M, Roulet E, Rovero A, Ruehl P, Saffi S, Saftoiu A, Salamida F, Salazar H, Salina G, Sanabria Gomez J, Sánchez F, Santos E, Santos E, Sarazin F, Sarmento R, Sarmiento-Cano C, Sato R, Savina P, Schauer M, Scherini V, Schieler H, Schimassek M, Schimp M, Schlüter F, Schmidt D, Scholten O, Schovánek P, Schröder F, Schröder S, Schumacher J, Sciutto S, Scornavacche M, Shellard R, Sigl G, Silli G, Sima O, Šmída R, Snow G, Sommers P, Soriano J, Souchard J, Squartini R, Stanca D, Stanič S, Stasielak J, Stassi P, Stolpovskiy M, Streich A, Suarez F, Suárez-Durán M, Sudholz T, Suomijärvi T, Supanitsky A, Šupík J, Szadkowski Z, Taboada A, Taborda O, Tapia A, Timmermans C, Todero Peixoto C, Tomé B, Torralba Elipe G, Travaini A, Travnicek P, Trini M, Tueros M, Ulrich R, Unger M, Urban M, Valdés Galicia J, Valiño I, Valore L, van Bodegom P, van den Berg A, van Vliet A, Varela E, Vargas Cárdenas B, Veberič D, Ventura C, Vergara Quispe I, Verzi V, Vicha J, Villaseñor L, Vink J, Vorobiov S, Wahlberg H, Watson A, Weber M, Weindl A, Wiedeński M, Wiencke L, Wilczyński H, Winchen T, Wirtz M, Wittkowski D, Wundheiler B, Yang L, Yushkov A, Zas E, Zavrtanik D, Zavrtanik M, Zehrer L, Zepeda A, Zimmermann B, Ziolkowski M, Zong Z, Zuccarello F. Data-driven estimation of the invisible energy of cosmic ray showers with the Pierre Auger Observatory. Int J Clin Exp Med 2019. [DOI: 10.1103/physrevd.100.082003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Correa A, Connolly D, Balcioglu M, Wu HT, Dashner S, Shchegrova S, Kalashnikova E, Pawar H, Uzzo R, Gong Y, Kister D, Collins M, Donovan M, Winters R, Aleshin A, Sethi H, Salari R, Louie M, Zimmermann B, Abbosh P. Presence of circulating tumour DNA in surgically resected renal cell carcinoma is associated with advanced disease and poor patient prognosis. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz239.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Jacobs S, Sethi H, Kolveska T, George T, Shchegrova S, Tin T, Lee J, Olson A, Renner D, Kalashnikova E, Yothers G, Wolmark N, Pogue-Geile K, Srinivasan A, Kortmansky J, Louie M, Salari R, Zimmermann B, Aleshin A, Allegra C. Analysis of circulating tumour DNA for early relapse detection in stage III colorectal cancer after adjuvant chemotherapy. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz239.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Lim R, Sugino T, Nolte H, Andrade J, Zimmermann B, Shi C, Doddaballapur A, Ong YT, Wilhelm K, Fasse JWD, Ernst A, Kaulich M, Husnjak K, Boettger T, Guenther S, Braun T, Krüger M, Benedito R, Dikic I, Potente M. Deubiquitinase USP10 regulates Notch signaling in the endothelium. Science 2019; 364:188-193. [PMID: 30975888 DOI: 10.1126/science.aat0778] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/14/2019] [Indexed: 12/15/2022]
Abstract
Notch signaling is a core patterning module for vascular morphogenesis that codetermines the sprouting behavior of endothelial cells (ECs). Tight quantitative and temporal control of Notch activity is essential for vascular development, yet the details of Notch regulation in ECs are incompletely understood. We found that ubiquitin-specific peptidase 10 (USP10) interacted with the NOTCH1 intracellular domain (NICD1) to slow the ubiquitin-dependent turnover of this short-lived form of the activated NOTCH1 receptor. Accordingly, inactivation of USP10 reduced NICD1 abundance and stability and diminished Notch-induced target gene expression in ECs. In mice, the loss of endothelial Usp10 increased vessel sprouting and partially restored the patterning defects caused by ectopic expression of NICD1. Thus, USP10 functions as an NICD1 deubiquitinase that fine-tunes endothelial Notch responses during angiogenic sprouting.
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Affiliation(s)
- R Lim
- Angiogenesis and Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany
| | - T Sugino
- Angiogenesis and Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany
| | - H Nolte
- Institute for Genetics and Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, D-50931 Cologne, Germany
| | - J Andrade
- Angiogenesis and Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany
| | - B Zimmermann
- Angiogenesis and Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany
| | - C Shi
- Angiogenesis and Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany
| | - A Doddaballapur
- Angiogenesis and Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany
| | - Y T Ong
- Angiogenesis and Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany
| | - K Wilhelm
- Angiogenesis and Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany
| | - J W D Fasse
- Angiogenesis and Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany
| | - A Ernst
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, D-60590 Frankfurt am Main, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, D-60590 Frankfurt am Main, Germany
| | - M Kaulich
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, D-60590 Frankfurt am Main, Germany
| | - K Husnjak
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, D-60590 Frankfurt am Main, Germany
| | - T Boettger
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany
| | - S Guenther
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany
| | - T Braun
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany
| | - M Krüger
- Institute for Genetics and Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, D-50931 Cologne, Germany
| | - R Benedito
- Molecular Genetics of Angiogenesis Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - I Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, D-60590 Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University, D-60438 Frankfurt am Main, Germany
| | - M Potente
- Angiogenesis and Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany. .,DZHK (German Center for Cardiovascular Research), partner site Frankfurt Rhine-Main, D-13347 Berlin, Germany.,International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
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Seddon AWR, Festi D, Robson TM, Zimmermann B. Fossil pollen and spores as a tool for reconstructing ancient solar-ultraviolet irradiance received by plants: an assessment of prospects and challenges using proxy-system modelling. Photochem Photobiol Sci 2019; 18:275-294. [PMID: 30649121 DOI: 10.1039/c8pp00490k] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Ultraviolet-B radiation (UV-B, 280-315 nm) constitutes less than 1% of the total solar radiation that reaches the Earth's surface but has a disproportional impact on biological and ecological processes from the individual to the ecosystem level. Absorption of UV-B by ozone is also one of the primary heat sources to the stratosphere, so variations in UV-B have important relationships to the Earth's radiation budget. Yet despite its importance for understanding atmospheric and ecological processes, there is limited understanding about the changes in UV-B radiation in the geological past. This is because systematic measurements of total ozone and surface UV-B only exist since the 1970s, so biological or geochemical proxies from sediment archives are needed to reconstruct UV-B irradiance received at the Earth surface beyond the experimental record. Recent developments have shown that the quantification of UV-B-absorbing compounds in pollen and spores have the potential to provide a continuous record of the solar-ultraviolet radiation received by plants. There is increasing interest in developing this proxy in palaeoclimatic and palaeoecological research. However, differences in interpretation exist between palaeoecologists, who are beginning to apply the proxy under various geological settings, and UV-B ecologists, who question whether a causal dose-response relationship of pollen and spore chemistry to UV-B irradiance has really been established. Here, we use a proxy-system modelling approach to systematically assess components of the pollen- and spore-based UV-B-irradiance proxy to ask how these differences can be resolved. We identify key unknowns and uncertainties in making inferences about past UV-B irradiance, from the pollen sensor, the sedimentary archive, and through the laboratory and experimental procedures in order to target priority areas of future work. We argue that an interdisciplinary approach, modifying methods used by plant ecologists studying contemporary responses to solar-UV-B radiation specifically to suit the needs of palaeoecological analyses, provides a way forward in developing the most reliable reconstructions for the UV-B irradiance received by plants across a range of timescales.
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Affiliation(s)
- Alistair W R Seddon
- Department of Biological Sciences, University of Bergen, Norway. .,Bjerknes Centre for Climate Research, University of Bergen, Norway.
| | - Daniela Festi
- Department of Botany, University of Innsbruck, Austria.,Faculty of Science and Technology, Free University of Bozen-Bolzano, Italy
| | - T Matthew Robson
- Organismal and Evolutionary Biology (OEB), Viikki Plant Science Centre (ViPS), Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Norway
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Innes SN, Arve LE, Zimmermann B, Nybakken L, Melby TI, Solhaug KA, Olsen JE, Torre S. Elevated air humidity increases UV mediated leaf and DNA damage in pea (Pisum sativum) due to reduced flavonoid content and antioxidant power. Photochem Photobiol Sci 2019; 18:387-399. [PMID: 30480699 DOI: 10.1039/c8pp00401c] [Citation(s) in RCA: 5] [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: 09/12/2018] [Accepted: 11/15/2018] [Indexed: 11/21/2022]
Abstract
Growth in high relative air humidity (RH, >85%) affects plant morphology and causes diminished response to stomatal closing signals. Many greenhouses are prone to high RH conditions, which may negatively affect production and post-harvest quality. UV radiation induces stomatal closure in several species, and facilitates disease control. We hypothesised that UV exposure may trigger stomatal closure in pea plants (Pisum sativum) grown in high RH, thereby restoring stomatal function. The effects of UV exposure were tested on plants grown in moderate (60%) or high (90%) RH. UV exposure occurred at night, according to a disease control protocol. Lower stomatal conductance rates were found in UV-exposed plants, though UV exposure did not improve the rate of response to closing stimuli or desiccation tolerance. UV-exposed plants showed leaf curling, chlorosis, necrosis, and DNA damage measured by the presence of cyclobutane pyrimidine dimers (CPD), all of which were significantly greater in high RH plants. These plants also had lower total flavonoid content than moderate RH plants, and UV-exposed plants had less than controls. Plants exposed to UV had a higher content of cuticular layer uronic compounds than control plants. However, high RH plants had a higher relative amount of cuticular waxes, but decreased proteins and uronic compounds. Plants grown in high RH had reduced foliar antioxidant power compared to moderate RH. These results indicate that high RH plants were more susceptible to UV-induced damage than moderate RH plants due to reduced flavonoid content and oxidative stress defence.
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Affiliation(s)
- Sheona N Innes
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway
- CERAD, Norwegian University of Life Sciences, Ås, 1430, Norway
| | - Louise E Arve
- The Norwegian Food Safety Authority, Brumundal, 2831, Norway
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, 1430, Norway
| | - Line Nybakken
- CERAD, Norwegian University of Life Sciences, Ås, 1430, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, 1430, Norway
| | - Tone I Melby
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway
| | - Knut Asbjørn Solhaug
- CERAD, Norwegian University of Life Sciences, Ås, 1430, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, 1430, Norway
| | - Jorunn E Olsen
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway
- CERAD, Norwegian University of Life Sciences, Ås, 1430, Norway
| | - Sissel Torre
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway.
- CERAD, Norwegian University of Life Sciences, Ås, 1430, Norway.
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Diehn S, Zimmermann B, Tafintseva V, Seifert S, Bağcıoğlu M, Ohlson M, Weidner S, Fjellheim S, Kohler A, Kneipp J. Combining Chemical Information From Grass Pollen in Multimodal Characterization. Front Plant Sci 2019; 10:1788. [PMID: 32082348 PMCID: PMC7005252 DOI: 10.3389/fpls.2019.01788] [Citation(s) in RCA: 5] [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] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/20/2019] [Indexed: 05/06/2023]
Abstract
The analysis of pollen chemical composition is important to many fields, including agriculture, plant physiology, ecology, allergology, and climate studies. Here, the potential of a combination of different spectroscopic and spectrometric methods regarding the characterization of small biochemical differences between pollen samples was evaluated using multivariate statistical approaches. Pollen samples, collected from three populations of the grass Poa alpina, were analyzed using Fourier-transform infrared (FTIR) spectroscopy, Raman spectroscopy, surface enhanced Raman scattering (SERS), and matrix assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS). The variation in the sample set can be described in a hierarchical framework comprising three populations of the same grass species and four different growth conditions of the parent plants for each of the populations. Therefore, the data set can work here as a model system to evaluate the classification and characterization ability of the different spectroscopic and spectrometric methods. ANOVA Simultaneous Component Analysis (ASCA) was applied to achieve a separation of different sources of variance in the complex sample set. Since the chosen methods and sample preparations probe different parts and/or molecular constituents of the pollen grains, complementary information about the chemical composition of the pollen can be obtained. By using consensus principal component analysis (CPCA), data from the different methods are linked together. This enables an investigation of the underlying global information, since complementary chemical data are combined. The molecular information from four spectroscopies was combined with phenotypical information gathered from the parent plants, thereby helping to potentially link pollen chemistry to other biotic and abiotic parameters.
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Affiliation(s)
- Sabrina Diehn
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
- BAM Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Valeria Tafintseva
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Stephan Seifert
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
- BAM Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Murat Bağcıoğlu
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Mikael Ohlson
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Steffen Weidner
- BAM Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Siri Fjellheim
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
- Nofima AS, Ås, Norway
| | - Janina Kneipp
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
- BAM Federal Institute for Materials Research and Testing, Berlin, Germany
- *Correspondence: Janina Kneipp,
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Kowalczyk J, Numata J, Zimmermann B, Klinger R, Habedank F, Just P, Schafft H, Lahrssen-Wiederholt M. Suitability of Wild Boar (Sus scrofa) as a Bioindicator for Environmental Pollution with Perfluorooctanoic Acid (PFOA) and Perfluorooctanesulfonic Acid (PFOS). Arch Environ Contam Toxicol 2018; 75:594-606. [PMID: 30116839 DOI: 10.1007/s00244-018-0552-8] [Citation(s) in RCA: 15] [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: 09/07/2017] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
Wildlife species, such as roe deer, moose, brown hare, wild boar, etc., are known to accumulate persistent environmental contaminants and thus are useful as bioindicators for environmental pollution. Wild boars become exposed to perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) from flora, fauna, water, and soil. The main exposure pathway to PFOA and PFOS is assumed to be the oral intake. From studies in domestic pigs (belonging to the same species Sus scrofa), it has been established that the oral exposure results in the liver accumulation of PFOA and PFOS. Thus, we posit that wild boars can be quantitatively used as suitable bioindicators for the presence of these substances in the environment. After the environmental pollution case in the Hessian region Sauerland in 2006, monitoring programs of individual Federal States from 2007 to 2013 showed that almost all wild boar liver samples contained PFOA and PFOS. In 2014, the analyses of PFOA and PFOS in liver of wild boars hunted in the south, north, and west of Germany showed liver concentrations at the same level among regions. Overall, an average ratio of PFOS:PFOA concentration in liver of 20.5:1 was found. To estimate the actual ratio of PFOS:PFOA in the wild boars' dietary exposure, we performed toxicokinetic modeling. According to the model, the PFOS exposure is only 2.2 times that of PFOA (because PFOS has slower elimination kinetics and higher affinity for the liver than PFOA). Overall, the determination of PFOA and PFOS in liver of wild boars indicates that both substances are ubiquitously distributed in the environment. At the same time, higher exposures were found for animals living in closer proximity to dense human populations.
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Affiliation(s)
- J Kowalczyk
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany.
| | - J Numata
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - B Zimmermann
- Bavarian Health and Food Safety Authority, Veterinärstr. 2, 85764, Oberschleißheim, Germany
| | - R Klinger
- Bavarian Health and Food Safety Authority, Veterinärstr. 2, 85764, Oberschleißheim, Germany
| | - F Habedank
- State Office of Agriculture, Food Safety and Fisheries, Thierfelderstr. 18, 18059, Rostock, Germany
| | - P Just
- Chemical and Veterinary Analytical Institute (CVUA) Westfalen, Westhoffstr. 17, 44791, Bochum, Germany
| | - H Schafft
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - M Lahrssen-Wiederholt
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
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Blümel R, Lukacs R, Zimmermann B, Bağcıoğlu M, Kohler A. Observation of Mie ripples in the synchrotron Fourier transform infrared spectra of spheroidal pollen grains. J Opt Soc Am A Opt Image Sci Vis 2018; 35:1769-1779. [PMID: 30462098 DOI: 10.1364/josaa.35.001769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/13/2018] [Indexed: 06/09/2023]
Abstract
Conceptually, biological cells are dielectric, photonic resonators that are expected to show a rich variety of shape resonances when exposed to electromagnetic radiation. For spheroidal cells, these shape resonances may be predicted and analyzed using the Mie theory of dielectric spheres, which predicts that a special class of resonances, i.e., whispering gallery modes (WGMs), causes ripples in the absorbance spectra of spheroidal cells. Indeed, the first tentative indication of the presence of Mie ripples in the synchrotron Fourier transform infrared (SFTIR) absorbance spectra of Juniperus chinensis pollen has already been reported [Analyst140, 3273 (2015)ANLYAG0365-488510.1039/C5AN00401B]. To show that this observation is no isolated incidence, but a generic spectral feature that can be expected to occur in all spheroidal biological cells, we measured and analyzed the SFTIR absorbance spectra of Cunninghamia lanceolata, Juniperus chinensis, Juniperus communis, and Juniperus excelsa. All four pollen species show Mie ripples. Since the WGMs causing the ripples are surface modes, we propose ripple spectroscopy as a powerful tool for studying the surface properties of spheroidal biological cells. In addition, our paper draws attention to the fact that shape resonances need to be taken into account when analyzing (S)FTIR spectra of isolated biological cells since shape resonances may distort the shape or mimic the presence of chemical absorption bands.
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Reinert T, Henriksen T, Rasmussen M, Sethi H, Salari R, Shchegrova S, Swenerton R, Wu HT, Sharma S, Christensen E, Natarajan P, Dashner S, Tin T, Olson A, Pawar H, Zimmermann B, Iversen L, Madsen M, Lin J, Andersen C. Serial circulating tumor DNA analysis for detection of residual disease, assessment of adjuvant therapy efficacy and for early recurrence detection in colorectal cancer. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy281.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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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Birkenkamp-Demtröder K, Christensen E, Sethi H, Sharma S, Wu HT, Taber A, Agerbæk M, Swenerton R, Salari R, Hafez D, Nordentoft I, Lamy P, Srinivasan R, Balcioglu M, Navarro S, Assaf Z, Zimmermann B, Lin J, Bjerggaard Jensen J, Dyrskjøt L. Longitudinal assessment of multiplex patient-specific ctDNA biomarkers in bladder cancer for diagnosis, surveillance and recurrence. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy269.084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Guo S, Kohler A, Zimmermann B, Heinke R, Stöckel S, Rösch P, Popp J, Bocklitz T. Extended Multiplicative Signal Correction Based Model Transfer for Raman Spectroscopy in Biological Applications. Anal Chem 2018; 90:9787-9795. [PMID: 30016081 DOI: 10.1021/acs.analchem.8b01536] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The chemometric analysis of Raman spectra of biological materials is hampered by spectral variations due to the instrumental setup that overlay the subtle biological changes of interest. Thus, an established statistical model may fail when applied to Raman spectra of samples acquired with a different device. Therefore, model transfer strategies are essential. Herein we report a model transfer approach based on extended multiplicative signal correction (EMSC). As opposed to existing model transfer methods, the EMSC based approach does not require group information on the secondary data sets, thus no extra measurements are required. The proposed model-transfer approach is a preprocessing procedure and can be combined with any method for regression and classification. The performance of EMSC as a model transfer method was demonstrated with a data set of Raman spectra of three Bacillus bacteria spore species ( B. mycoides, B. subtilis, and B. thuringiensis), which were acquired on four Raman spectrometers. A three-group classification by partial least-squares discriminant analysis (PLS-DA) with leave-one-device-out external cross-validation (LODCV) was performed. The mean sensitivities of the prediction on the independent device were considerably improved by the EMSC method. Besides the mean sensitivity, the model transferability was additionally benchmarked by the newly defined numeric markers: (1) relative Pearson's correlation coefficient and (2) relative Fisher's discriminant ratio. We show that these markers have led to consistent conclusions compared to the mean sensitivity of the classification. The advantage of our defined markers is that the evaluation is more effective and objective, because it is independent of the classification models.
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Affiliation(s)
- Shuxia Guo
- Institute of Physical Chemistry and Abbe Center of Photonics , Friedrich Schiller University of Jena , Helmholtzweg 4 , D-07743 Jena , Germany.,Leibniz Institute of Photonic Technology, Member of Leibniz Research Alliance 'Health Technologies' , Albert-Einstein-Straße 9 , D-07745 Jena , Germany
| | - Achim Kohler
- Faculty of Science and Technology , Norwegian University of Life Sciences , P.O. Box 5003, NO1432 , Ås , Norway
| | - Boris Zimmermann
- Faculty of Science and Technology , Norwegian University of Life Sciences , P.O. Box 5003, NO1432 , Ås , Norway
| | - Ralf Heinke
- Institute of Physical Chemistry and Abbe Center of Photonics , Friedrich Schiller University of Jena , Helmholtzweg 4 , D-07743 Jena , Germany
| | - Stephan Stöckel
- Institute of Physical Chemistry and Abbe Center of Photonics , Friedrich Schiller University of Jena , Helmholtzweg 4 , D-07743 Jena , Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics , Friedrich Schiller University of Jena , Helmholtzweg 4 , D-07743 Jena , Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics , Friedrich Schiller University of Jena , Helmholtzweg 4 , D-07743 Jena , Germany.,Leibniz Institute of Photonic Technology, Member of Leibniz Research Alliance 'Health Technologies' , Albert-Einstein-Straße 9 , D-07745 Jena , Germany.,InfectoGnostics , Forschungscampus Jena , Philosophenweg 7 , D-07743 Jena , Germany
| | - Thomas Bocklitz
- Institute of Physical Chemistry and Abbe Center of Photonics , Friedrich Schiller University of Jena , Helmholtzweg 4 , D-07743 Jena , Germany.,Leibniz Institute of Photonic Technology, Member of Leibniz Research Alliance 'Health Technologies' , Albert-Einstein-Straße 9 , D-07745 Jena , Germany
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Kosa G, Vuoristo KS, Horn SJ, Zimmermann B, Afseth NK, Kohler A, Shapaval V. Assessment of the scalability of a microtiter plate system for screening of oleaginous microorganisms. Appl Microbiol Biotechnol 2018; 102:4915-4925. [PMID: 29644428 PMCID: PMC5954000 DOI: 10.1007/s00253-018-8920-x] [Citation(s) in RCA: 24] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 02/19/2018] [Accepted: 03/07/2018] [Indexed: 12/01/2022]
Abstract
Recent developments in molecular biology and metabolic engineering have resulted in a large increase in the number of strains that need to be tested, positioning high-throughput screening of microorganisms as an important step in bioprocess development. Scalability is crucial for performing reliable screening of microorganisms. Most of the scalability studies from microplate screening systems to controlled stirred-tank bioreactors have been performed so far with unicellular microorganisms. We have compared cultivation of industrially relevant oleaginous filamentous fungi and microalga in a Duetz-microtiter plate system to benchtop and pre-pilot bioreactors. Maximal glucose consumption rate, biomass concentration, lipid content of the biomass, biomass, and lipid yield values showed good scalability for Mucor circinelloides (less than 20% differences) and Mortierella alpina (less than 30% differences) filamentous fungi. Maximal glucose consumption and biomass production rates were identical for Crypthecodinium cohnii in microtiter plate and benchtop bioreactor. Most likely due to shear stress sensitivity of this microalga in stirred bioreactor, biomass concentration and lipid content of biomass were significantly higher in the microtiter plate system than in the benchtop bioreactor. Still, fermentation results obtained in the Duetz-microtiter plate system for Crypthecodinium cohnii are encouraging compared to what has been reported in literature. Good reproducibility (coefficient of variation less than 15% for biomass growth, glucose consumption, lipid content, and pH) were achieved in the Duetz-microtiter plate system for Mucor circinelloides and Crypthecodinium cohnii. Mortierella alpina cultivation reproducibility might be improved with inoculation optimization. In conclusion, we have presented suitability of the Duetz-microtiter plate system for the reproducible, scalable, and cost-efficient high-throughput screening of oleaginous microorganisms.
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Affiliation(s)
- Gergely Kosa
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway.
| | - Kiira S Vuoristo
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway
| | - Svein Jarle Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway
| | | | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway
| | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway
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Kosa G, Zimmermann B, Kohler A, Ekeberg D, Afseth NK, Mounier J, Shapaval V. High-throughput screening of Mucoromycota fungi for production of low- and high-value lipids. Biotechnol Biofuels 2018; 11:66. [PMID: 29563969 PMCID: PMC5851148 DOI: 10.1186/s13068-018-1070-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 03/07/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND Mucoromycota fungi are important producers of low- and high-value lipids. Mortierella alpina is used for arachidonic acid production at industrial scale. In addition, oleaginous Mucoromycota fungi are promising candidates for biodiesel production. A critical step in the development of such biotechnological applications is the selection of suitable strains for lipid production. The aim of the present study was to use the Duetz-microtiter plate system combined with Fourier transform infrared (FTIR) spectroscopy for high-throughput screening of the potential of 100 Mucoromycota strains to produce low- and high-value lipids. RESULTS With this reproducible, high-throughput method, we found several promising strains for high-value omega-6 polyunsaturated fatty acid (PUFA) and biodiesel production purposes. Gamma-linolenic acid content was the highest in Mucor fragilis UBOCC-A-109196 (24.5% of total fatty acids), and Cunninghamella echinulata VKM F-470 (24.0%). For the first time, we observed concomitant gamma-linolenic acid and alpha-linolenic acid (up to 13.0%) production in psychrophilic Mucor flavus strains. Arachidonic acid was present the highest amount in M. alpina ATCC 32222 (41.1% of total fatty acids). Low cultivation temperature (15 °C) activated the temperature sensitive ∆17 desaturase enzyme in Mortierella spp., resulting in eicosapentaenoic acid production with up to 11.0% of total fatty acids in M. humilis VKM F-1494. Cunninghamella blakesleeana CCM-705, Umbelopsis vinacea CCM F-539 and UBOCC-A-101347 showed very good growth (23-26 g/L) and lipid production (7.0-8.3 g/L) with high palmitic and oleic acid, and low PUFA content, which makes them attractive candidates for biodiesel production. Absidia glauca CCM 451 had the highest total lipid content (47.2% of biomass) of all tested strains. We also demonstrated the potential of FTIR spectroscopy for high-throughput screening of total lipid content of oleaginous fungi. CONCLUSIONS The use of Duetz-microtiter plate system combined with FTIR spectroscopy and multivariate analysis, is a feasible approach for high-throughput screening of lipid production in Mucoromycota fungi. Several promising strains have been identified by this method for the production of high-value PUFA and biodiesel.
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Affiliation(s)
- Gergely Kosa
- Faculty of Science and Technology, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Dag Ekeberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | | | - Jerome Mounier
- Université de Brest, EA3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest Iroise, 29280 Plouzané, France
| | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
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Zimmermann B. Chemical characterization and identification of Pinaceae pollen by infrared microspectroscopy. Planta 2018; 247:171-180. [PMID: 28913637 DOI: 10.1007/s00425-017-2774-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 03/23/2017] [Accepted: 09/08/2017] [Indexed: 05/24/2023]
Abstract
FTIR microspectroscopy, in combination with spectral averaging procedure, enables precise analysis of pollen grains for chemical characterization and identification studies of fresh and fossilised pollen in botany, ecology and palaeosciences. Infrared microspectroscopy (µFTIR) of Pinaceae pollen can provide valuable information on plant phenology, ecophysiology and paleoecology, but measurements are challenging, resulting in unreproducible spectra. The comparative analysis of µFTIR spectra belonging to morphologically different Pinaceae pollen, namely bisaccate Pinus and monosaccate Tsuga pollen, was conducted. The study shows that the main cause of spectral variability is non-radial symmetry of bisaccate pollen grains, while additional variation is caused by Mie scattering. Averaging over relatively small number of single pollen grain spectra (approx. 5-10) results with reproducible data on pollen chemical composition. The practical applicability of the µFTIR spectral averaging method has been demonstrated by the partial least-squares regression-based differentiation of the two closely related Pinus species with morphologically indistinguishable pollen: Pinus mugo (mountain pine) and Pinus sylvestris (Scots pine). The study has demonstrated that the µFTIR approach can be used for identification, differentiation and chemical characterization of pollen with complex morphology. The methodology enables analysis of fresh pollen, as well as fossil pollen from sediment core samples, and can be used in botany, ecology and paleoecology for study of biotic and abiotic effects on plants.
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Affiliation(s)
- Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, 1432, Ås, Norway.
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Aab A, Abreu P, Aglietta M, Al Samarai I, Albuquerque I, Allekotte I, Almela A, Alvarez Castillo J, Alvarez-Muñiz J, Anastasi G, Anchordoqui L, Andrada B, Andringa S, Aramo C, Arqueros F, Arsene N, Asorey H, Assis P, Aublin J, Avila G, Badescu A, Balaceanu A, Barbato F, Barreira Luz R, Beatty J, Becker K, Bellido J, Berat C, Bertaina M, Bertou X, Biermann P, Biteau J, Blaess S, Blanco A, Blazek J, Bleve C, Boháčová M, Boncioli D, Bonifazi C, Borodai N, Botti A, Brack J, Brancus I, Bretz T, Bridgeman A, Briechle F, Buchholz P, Bueno A, Buitink S, Buscemi M, Caballero-Mora K, Caccianiga L, Cancio A, Canfora F, Caramete L, Caruso R, Castellina A, Catalani F, Cataldi G, Cazon L, Chavez A, Chinellato J, Chudoba J, Clay R, Cobos A, Colalillo R, Coleman A, Collica L, Coluccia M, Conceição R, Consolati G, Contreras F, Cooper M, Coutu S, Covault C, Cronin J, D’Amico S, Daniel B, Dasso S, Daumiller K, Dawson B, de Almeida R, de Jong S, De Mauro G, de Mello Neto J, De Mitri I, de Oliveira J, de Souza V, Debatin J, Deligny O, Díaz Castro M, Diogo F, Dobrigkeit C, D’Olivo J, Dorosti Q, dos Anjos R, Dova M, Dundovic A, Ebr J, Engel R, Erdmann M, Erfani M, Escobar C, Espadanal J, Etchegoyen A, Falcke H, Farmer J, Farrar G, Fauth A, Fazzini N, Fenu F, Fick B, Figueira J, Filipčič A, Fratu O, Freire M, Fujii T, Fuster A, Gaior R, García B, Garcia-Pinto D, Gaté F, Gemmeke H, Gherghel-Lascu A, Ghia P, Giaccari U, Giammarchi M, Giller M, Głas D, Glaser C, Golup G, Gómez Berisso M, Gómez Vitale P, González N, Gorgi A, Gorham P, Grillo A, Grubb T, Guarino F, Guedes G, Halliday R, Hampel M, Hansen P, Harari D, Harrison T, Harton J, Haungs A, Hebbeker T, Heck D, Heimann P, Herve A, Hill G, Hojvat C, Holt E, Homola P, Hörandel J, Horvath P, Hrabovský M, Huege T, Hulsman J, Insolia A, Isar P, Jandt I, Johnsen J, Josebachuili M, Jurysek J, Kääpä A, Kambeitz O, Kampert K, Keilhauer B, Kemmerich N, Kemp E, Kemp J, Kieckhafer R, Klages H, Kleifges M, Kleinfeller J, Krause R, Krohm N, Kuempel D, Kukec Mezek G, Kunka N, Kuotb Awad A, Lago B, LaHurd D, Lang R, Lauscher M, Legumina R, Leigui de Oliveira M, Letessier-Selvon A, Lhenry-Yvon I, Link K, Lo Presti D, Lopes L, López R, López Casado A, Lorek R, Luce Q, Lucero A, Malacari M, Mallamaci M, Mandat D, Mantsch P, Mariazzi A, Mariş I, Marsella G, Martello D, Martinez H, Martínez Bravo O, Masías Meza J, Mathes H, Mathys S, Matthews J, Matthews J, Matthiae G, Mayotte E, Mazur P, Medina C, Medina-Tanco G, Melo D, Menshikov A, Merenda KD, Michal S, Micheletti M, Middendorf L, Miramonti L, Mitrica B, Mockler D, Mollerach S, Montanet F, Morello C, Mostafá M, Müller A, Müller G, Muller M, Müller S, Mussa R, Naranjo I, Nellen L, Nguyen P, Niculescu-Oglinzanu M, Niechciol M, Niemietz L, Niggemann T, Nitz D, Nosek D, Novotny V, Nožka L, Núñez L, Ochilo L, Oikonomou F, Olinto A, Palatka M, Pallotta J, Papenbreer P, Parente G, Parra A, Paul T, Pech M, Pedreira F, Pękala J, Pelayo R, Peña-Rodriguez J, Pereira L, Perlin M, Perrone L, Peters C, Petrera S, Phuntsok J, Piegaia R, Pierog T, Pimenta M, Pirronello V, Platino M, Plum M, Porowski C, Prado R, Privitera P, Prouza M, Quel E, Querchfeld S, Quinn S, Ramos-Pollan R, Rautenberg J, Ravignani D, Ridky J, Riehn F, Risse M, Ristori P, Rizi V, Rodrigues de Carvalho W, Rodriguez Fernandez G, Rodriguez Rojo J, Rogozin D, Roncoroni M, Roth M, Roulet E, Rovero A, Ruehl P, Saffi S, Saftoiu A, Salamida F, Salazar H, Saleh A, Salesa Greus F, Salina G, Sánchez F, Sanchez-Lucas P, Santos E, Santos E, Sarazin F, Sarmento R, Sarmiento-Cano C, Sato R, Schauer M, Scherini V, Schieler H, Schimp M, Schmidt D, Scholten O, Schovánek P, Schröder F, Schröder S, Schulz A, Schumacher J, Sciutto S, Segreto A, Shadkam A, Shellard R, Sigl G, Silli G, Sima O, Śmiałkowski A, Šmída R, Smith B, Snow G, Sommers P, Sonntag S, Squartini R, Stanca D, Stanič S, Stasielak J, Stassi P, Stolpovskiy M, Strafella F, Streich A, Suarez F, Suarez Durán M, Sudholz T, Suomijärvi T, Supanitsky A, Šupík J, Swain J, Szadkowski Z, Taboada A, Taborda O, Theodoro V, Timmermans C, Todero Peixoto C, Tomankova L, Tomé B, Torralba Elipe G, Travnicek P, Trini M, Ulrich R, Unger M, Urban M, Valdés Galicia J, Valiño I, Valore L, van Aar G, van Bodegom P, van den Berg A, van Vliet A, Varela E, Vargas Cárdenas B, Varner G, Vázquez R, Veberič D, Ventura C, Vergara Quispe I, Verzi V, Vicha J, Villaseñor L, Vorobiov S, Wahlberg H, Wainberg O, Walz D, Watson A, Weber M, Weindl A, Wiencke L, Wilczyński H, Wileman C, Wirtz M, Wittkowski D, Wundheiler B, Yang L, Yushkov A, Zas E, Zavrtanik D, Zavrtanik M, Zepeda A, Zimmermann B, Ziolkowski M, Zong Z, Zuccarello F. Inferences on mass composition and tests of hadronic interactions from 0.3 to 100 EeV using the water-Cherenkov detectors of the Pierre Auger Observatory. Int J Clin Exp Med 2017. [DOI: 10.1103/physrevd.96.122003] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Zimmermann B, Bağcıoğlu M, Tafinstseva V, Kohler A, Ohlson M, Fjellheim S. A high-throughput FTIR spectroscopy approach to assess adaptive variation in the chemical composition of pollen. Ecol Evol 2017; 7:10839-10849. [PMID: 29299262 PMCID: PMC5743575 DOI: 10.1002/ece3.3619] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/11/2017] [Indexed: 01/17/2023] Open
Abstract
The two factors defining male reproductive success in plants are pollen quantity and quality, but our knowledge about the importance of pollen quality is limited due to methodological constraints. Pollen quality in terms of chemical composition may be either genetically fixed for high performance independent of environmental conditions, or it may be plastic to maximize reproductive output under different environmental conditions. In this study, we validated a new approach for studying the role of chemical composition of pollen in adaptation to local climate. The approach is based on high-throughput Fourier infrared (FTIR) characterization and biochemical interpretation of pollen chemical composition in response to environmental conditions. The study covered three grass species, Poa alpina, Anthoxanthum odoratum, and Festuca ovina. For each species, plants were grown from seeds of three populations with wide geographic and climate variation. Each individual plant was divided into four genetically identical clones which were grown in different controlled environments (high and low levels of temperature and nutrients). In total, 389 samples were measured using a high-throughput FTIR spectrometer. The biochemical fingerprints of pollen were species and population specific, and plastic in response to different environmental conditions. The response was most pronounced for temperature, influencing the levels of proteins, lipids, and carbohydrates in pollen of all species. Furthermore, there is considerable variation in plasticity of the chemical composition of pollen among species and populations. The use of high-throughput FTIR spectroscopy provides fast, cheap, and simple assessment of the chemical composition of pollen. In combination with controlled-condition growth experiments and multivariate analyses, FTIR spectroscopy opens up for studies of the adaptive role of pollen that until now has been difficult with available methodology. The approach can easily be extended to other species and environmental conditions and has the potential to significantly increase our understanding of plant male function.
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Affiliation(s)
- Boris Zimmermann
- Faculty of Life Science and TechnologyNorwegian University of Life SciencesÅsNorway
| | - Murat Bağcıoğlu
- Faculty of Life Science and TechnologyNorwegian University of Life SciencesÅsNorway
| | - Valeria Tafinstseva
- Faculty of Life Science and TechnologyNorwegian University of Life SciencesÅsNorway
| | - Achim Kohler
- Faculty of Life Science and TechnologyNorwegian University of Life SciencesÅsNorway
- Nofima ASÅsNorway
| | - Mikael Ohlson
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesÅsNorway
| | - Siri Fjellheim
- Faculty of BiosciencesNorwegian University of Life SciencesÅsNorway
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Kosa G, Shapaval V, Kohler A, Zimmermann B. FTIR spectroscopy as a unified method for simultaneous analysis of intra- and extracellular metabolites in high-throughput screening of microbial bioprocesses. Microb Cell Fact 2017; 16:195. [PMID: 29132358 PMCID: PMC5683213 DOI: 10.1186/s12934-017-0817-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/08/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Analyses of substrate and metabolites are often bottleneck activities in high-throughput screening of microbial bioprocesses. We have assessed Fourier transform infrared spectroscopy (FTIR), in combination with high throughput micro-bioreactors and multivariate statistical analyses, for analysis of metabolites in high-throughput screening of microbial bioprocesses. In our previous study, we have demonstrated that high-throughput (HTS) FTIR can be used for estimating content and composition of intracellular metabolites, namely triglyceride accumulation in oleaginous filamentous fungi. As a continuation of that research, in the present study HTS FTIR was evaluated as a unified method for simultaneous quantification of intra- and extracellular metabolites and substrate consumption. As a proof of concept, a high-throughput microcultivation of oleaginous filamentous fungi was conducted in order to monitor production of citric acid (extracellular metabolite) and triglyceride lipids (intracellular metabolites), as well as consumption of glucose in the cultivation medium. RESULTS HTS FTIR analyses of supernatant samples was compared with an attenuated total reflection (ATR) FTIR, which is an established method for bioprocess monitoring. Glucose and citric acid content of growth media was quantified by high performance liquid chromatography (HPLC). Partial least square regression (PLSR) between HPLC glucose and citric acid data and the corresponding FTIR spectral data was used to set up calibration models. PLSR results for HTS measurements were very similar to the results obtained with ATR methodology, with high coefficients of determination (0.91-0.98) and low error values (4.9-8.6%) for both glucose and citric acid estimates. CONCLUSIONS The study has demonstrated that intra- and extracellular metabolites, as well as nutrients in the cultivation medium, can be monitored by a unified approach by HTS FTIR. The proof-of-concept study has validated that HTS FTIR, in combination with Duetz microtiter plate system and chemometrics, can be used for high throughput screening of microbial bioprocesses. It can be anticipated that the approach, demonstrated here on single-cell oil production by filamentous fungi, can find general application in screening studies of microbial bioprocesses, such as production of single-cell proteins, biopolymers, polysaccharides, carboxylic acids, and other type of metabolites.
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Affiliation(s)
- Gergely Kosa
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432 Ås, Norway
- Nofima AS, Osloveien 1, 1430 Ås, Norway
| | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432 Ås, Norway
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432 Ås, Norway
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432 Ås, Norway
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Koerner K, Sahlmen P, Zimmermann B, Cardoso M, Kubanek B. In vitro Platelet Function during Storage in Three Different Additive Solutions. Vox Sang 2017. [DOI: 10.1159/000462581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Kosa G, Kohler A, Tafintseva V, Zimmermann B, Forfang K, Afseth NK, Tzimorotas D, Vuoristo KS, Horn SJ, Mounier J, Shapaval V. Microtiter plate cultivation of oleaginous fungi and monitoring of lipogenesis by high-throughput FTIR spectroscopy. Microb Cell Fact 2017; 16:101. [PMID: 28599651 PMCID: PMC5466753 DOI: 10.1186/s12934-017-0716-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [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: 01/24/2017] [Accepted: 06/05/2017] [Indexed: 02/06/2023] Open
Abstract
Background Oleaginous fungi can accumulate lipids by utilizing a wide range of waste substrates. They are an important source for the industrial production of omega-6 polyunsaturated fatty acids (gamma-linolenic and arachidonic acid) and have been suggested as an alternative route for biodiesel production. Initial research steps for various applications include the screening of fungi in order to find efficient fungal producers with desired fatty acid composition. Traditional cultivation methods (shake flask) and lipid analysis (extraction-gas chromatography) are not applicable for large-scale screening due to their low throughput and time-consuming analysis. Here we present a microcultivation system combined with high-throughput Fourier transform infrared (FTIR) spectroscopy for efficient screening of oleaginous fungi. Results The microcultivation system enables highly reproducible fungal fermentations throughout 12 days of cultivation. Reproducibility was validated by FTIR and HPLC data. Analysis of FTIR spectral ester carbonyl peaks of fungal biomass offered a reliable high-throughput at-line method to monitor lipid accumulation. Partial least square regression between gas chromatography fatty acid data and corresponding FTIR spectral data was used to set up calibration models for the prediction of saturated fatty acids, monounsaturated fatty acids, polyunsaturated fatty acids, unsaturation index, total lipid content and main individual fatty acids. High coefficients of determination (R2 = 0.86–0.96) and satisfactory residual predictive deviation of cross-validation (RPDCV = 2.6–5.1) values demonstrated the goodness of these models. Conclusions We have demonstrated in this study, that the presented microcultivation system combined with rapid, high-throughput FTIR spectroscopy is a suitable screening platform for oleaginous fungi. Sample preparation for FTIR measurements can be automated to further increase throughput of the system. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0716-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gergely Kosa
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway.
| | - Achim Kohler
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway
| | - Valeria Tafintseva
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway
| | - Kristin Forfang
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway
| | | | | | - Kiira S Vuoristo
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway
| | - Svein Jarle Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway
| | - Jerome Mounier
- Université de Brest, EA3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest Iroise, 29280, Plouzané, France
| | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, Postbox 5003, 1432, Ås, Norway
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Farnsworth B, Radomska KJ, Zimmermann B, Kettunen P, Jazin E, Emilsson LS. QKI6B mRNA levels are upregulated in schizophrenia and predict GFAP expression. Brain Res 2017; 1669:63-68. [PMID: 28552414 DOI: 10.1016/j.brainres.2017.05.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 03/04/2017] [Revised: 05/21/2017] [Accepted: 05/22/2017] [Indexed: 01/21/2023]
Abstract
Schizophrenia is a highly heritable disorder with a heterogeneous symptomatology. Research increasingly indicates the importance of the crucial and often overlooked glial perturbations within schizophrenia. Within this study, we examined an isoform of quaking (a gene encoding an RNA-binding protein that is exclusively expressed in glial cells), known as QKI6B, and a prototypical astrocyte marker, glial fibrillary acidic protein (GFAP), postulated to be under the regulation of QKI. The expression levels of these genes were quantified across post-mortem brain samples from 55 schizophrenic individuals, and 55 healthy controls, using real-time PCR. We report, through an analysis of covariance (ANCOVA) model, an upregulation of both QKI6B, and GFAP in the prefrontal cortex of brain samples of schizophrenic individuals, as compared to control samples. Previous research has suggested that the QKI protein directly regulates the expression of several genes through interaction with a motif in the target's sequence, termed the Quaking Response Element (QRE). We therefore examined if QKI6B expression can predict the outcome of GFAP, and several oligodendrocyte-related genes, using a multiple linear regression approach. We found that QKI6B significantly predicts the expression of GFAP, but does not predict oligodendrocyte-related gene outcome, as previously seen with other QKI isoforms.
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Affiliation(s)
- B Farnsworth
- Department of Evolution and Development, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - K J Radomska
- Department of Evolution and Development, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - B Zimmermann
- Department of Evolution and Development, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - P Kettunen
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - E Jazin
- Department of Evolution and Development, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - L S Emilsson
- Department of Evolution and Development, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
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Forfang K, Zimmermann B, Kosa G, Kohler A, Shapaval V. FTIR Spectroscopy for Evaluation and Monitoring of Lipid Extraction Efficiency for Oleaginous Fungi. PLoS One 2017; 12:e0170611. [PMID: 28118388 PMCID: PMC5261814 DOI: 10.1371/journal.pone.0170611] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [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: 08/24/2016] [Accepted: 01/06/2017] [Indexed: 11/19/2022] Open
Abstract
To assess whether Fourier Transform Infrared (FTIR) spectroscopy could be used to evaluate and monitor lipid extraction processes, the extraction methods of Folch, Bligh and Lewis were used. Biomass of the oleaginous fungi Mucor circinelloides and Mortierella alpina were employed as lipid-rich material for the lipid extraction. The presence of lipids was determined by recording infrared spectra of all components in the lipid extraction procedure, such as the biomass before and after extraction, the water and extract phases. Infrared spectra revealed the incomplete extraction after all three extraction methods applied to M.circinelloides and it was shown that mechanical disruption using bead beating and HCl treatment were necessary to complete the extraction in this species. FTIR spectroscopy was used to identify components, such as polyphosphates, that may have negatively affected the extraction process and resulted in differences in extraction efficiency between M.circinelloides and M.alpina. Residual lipids could not be detected in the infrared spectra of M.alpina biomass after extraction using the Folch and Lewis methods, indicating their complete lipid extraction in this species. Bligh extraction underestimated the fatty acid content of both M.circinelloides and M.alpina biomass and an increase in the initial solvent-to-sample ratio (from 3:1 to 20:1) was needed to achieve complete extraction and a lipid-free IR spectrum. In accordance with previous studies, the gravimetric lipid yield was shown to overestimate the potential of the SCO producers and FAME quantification in GC-FID was found to be the best-suited method for lipid quantification. We conclude that FTIR spectroscopy can serve as a tool for evaluating the lipid extraction efficiency, in addition to identifying components that may affect lipid extraction processes.
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Affiliation(s)
- Kristin Forfang
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway
- Nofima AS, Ås, Norway
- * E-mail:
| | - Boris Zimmermann
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Gergely Kosa
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway
- Nofima AS, Ås, Norway
| | - Achim Kohler
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Volha Shapaval
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway
- Nofima AS, Ås, Norway
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