| 1. |
- Ferro, Lorenza, 1989-, et al.
(author)
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Statistical Methods for Rapid Quantification of Proteins, Lipids, and Carbohydrates in Nordic Microalgal Species Using ATR-FTIR Spectroscopy
- 2019
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In: Molecules. - : MDPI. - 1431-5157 .- 1420-3049. ; 24:18
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Journal article (peer-reviewed)abstract
- Attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy is a simple, cheap, and fast method to collect chemical compositional information from microalgae. However, (semi)quantitative evaluation of the collected data can be daunting. In this work, ATR-FTIR spectroscopy was used to monitor changes of protein, lipid, and carbohydrate content in seven green microalgae grown under nitrogen starvation. Three statistical methods-univariate linear regression analysis (ULRA), orthogonal partial least squares (OPLS), and multivariate curve resolution-alternating least squares (MCR-ALS)-were compared in their ability to model and predict the concentration of these compounds in the biomass. OPLS was found superior, since it i) included all three compounds simultaneously; ii) explained variations in the data very well; iii) had excellent prediction accuracy for proteins and lipids, and acceptable for carbohydrates; and iv) was able to discriminate samples based on cultivation stage and type of storage compounds accumulated in the cells. ULRA models worked well for the determination of proteins and lipids, but carbohydrates could only be estimated if already determined protein contents were used for scaling. Results obtained by MCR-ALS were similar to ULRA, however, this method is considerably easier to perform and interpret than the more abstract statistical/chemometric methods. FTIR-spectroscopy-based models allow high-throughput, cost-effective, and rapid estimation of biomass composition of green microalgae.
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| 2. |
- Ferro, Lorenza, et al.
(author)
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Subarctic microalgal strains treat wastewater and produce biomass at low temperature and short photoperiod
- 2018
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In: Algal Research. - : Elsevier. - 2211-9264. ; 35, s. 160-167
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Journal article (peer-reviewed)abstract
- In Northern countries, microalgal-based processes are challenging due to low light and temperature conditions during a significant part of the year. Three natural strains from Northern Sweden (Chlorella vulgaris, Scenedesmus sp., Desmodesmus sp.) and a collection strain (Scenedesmus obliquus UTEX 417) were cultured in municipal wastewater, comparing their performances, biomass composition and nutrients removal under continuous light at standard (25 °C) and low temperature (5 °C), short photoperiod (3 h light, 25 °C), or moderate winter conditions (6 h light, 15 °C). Only the natural strains grew at low temperature, highly consuming total nitrogen and phosphate (>80% and >70%, respectively) even during cold- and dark-stress. At reduced growth rates, C. vulgaris and Scenedesmus sp. produced similar amounts of biomass (>1 g/l) as in standard conditions. Scenedesmus sp. and Desmodesmus sp. showed phenotypic plasticity and increased carbohydrate content. Short photoperiod strongly reduced growth rates, biomass and storage compounds and induced flocculation in C. vulgaris.
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| 3. |
- Gillgren, Thomas, et al.
(author)
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A one-pot set-up for real-time reaction monitoring by FTIR spectroscopy
- 2016
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In: Wood Science and Technology. - : Springer Science and Business Media LLC. - 0043-7719 .- 1432-5225. ; 50:3, s. 567-580
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Journal article (peer-reviewed)abstract
- This paper presents a method for monitoring solution reactions in real time using Fourier transform infrared (FTIR) spectroscopy. Compared to batch measurements or flow-through systems, where the reaction and spectroscopic measurements are spatially and temporarily separated, this method enables continuous FTIR spectroscopic measurements of reactions without delay and directly in the reaction vessel. The strengths are demonstrated, and the limitations of the method are highlighted using the reaction of a lignin model compound and a sulphite salt. The method is capable of identifying both kinetic and thermodynamic properties (e.g. reaction speed, intermediate species), allowing rapid and cost-effective optimisation of reaction parameters. While specificity can be limited, the non-destructive nature of the method facilitates direct coupling to other techniques to help resolve potential ambiguities. The method is of general interest in wet chemistry applications and in several areas of the lignocellulosic biomass field in particular, as it can provide new insights into natural and industrial reactions and processes.
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| 4. |
- Gorzsás, András
(author)
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Chemical imaging of xylem by Raman microspectroscopy
- 2017. - 1
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In: Xylem. - New York : Humana Press. - 9781493967209 - 9781493967223 ; , s. 133-178
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Book chapter (peer-reviewed)abstract
- Raman microspectroscopic techniques provide highly detailed chemical information about xylem tissue at submicron spatial resolution. The techniques are generally sensitive and they provide a powerful, yet inexpensive way to probe the chemical composition of individual cells or cell wall layers in situ, non-destructively, in a confocal manner, simultaneously detecting all chemical compounds without the need of external agents (label, dyes, stains). Problems with limited specificity in complex chemical matrices such as cell walls may arise, compounded by fluorescence problems. However, these can often be circumvented. In this chapter, the basics of the technique, including a common instrumental setup, together with the general strengths and limitations of Raman microspectroscopy are discussed. Detailed protocols are provided for single point measurements, as well as for fully customizable raster scan mapping, including sample preparation, setup, and measurement steps. The major steps of the data analysis procedure are discussed as well.
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| 5. |
- Gorzsás, András
(author)
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Raman microspectroscopy
- 2018
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In: Encyclopedia of Geochemistry. - Cham : Springer. - 9783319393117 - 9783319393124 ; , s. 1303-1307
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Book chapter (peer-reviewed)
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| 6. |
- Gustafsson, Asa, et al.
(author)
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Isolation and characterization of a respirable particle fraction from residential house-dust
- 2018
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In: Environmental Research. - : Academic Press Inc Elsevier Science. - 0013-9351 .- 1096-0953. ; 161, s. 284-290
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Journal article (peer-reviewed)abstract
- Indoor air pollution has caused increasing concern in recent years. As we spend most of our lives indoors, it is crucial to understand the health effects caused by indoor air pollution. Household dust serve as good proxy for accessing indoor air pollution, especially smaller dust particles that can pass into the lungs are of interest. In this study we present an efficient method for the isolation of dust particles in the respirable size range. The respirable fraction was recovered from vacuum cleaner bags, separated by stepwise sieving, followed by characterization for size, morphology, surface area, organic content and elemental composition. The respirable fraction was obtained in a yield of 0.6% with a specific surface area of 2.5 m(2)/g and a Mass Median Aerodynamic Diameter of 3.73 +/- 0.15 mu m. Aluminum and zink were the dominating metals measured in the dust, whereas the major mineral components were found to be silicon dioxide and calcium carbonate. The fraction of organic matter in the dust was measured to be 69 +/- 1%. The organic matrix contained bacterial and fungi and a presence of skin fragments. We present here an efficient and fast method for the isolation of dust particles in the respirable size range. That is of considerable value due to the need for large quantities of respirable particle fractions to conduct toxicological studies and risk assessment work.
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| 7. |
- Kenney, Janice P. L., et al.
(author)
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Applications of Fourier-transform Infrared Spectroscopy in Geomicrobiology
- 2019
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In: Analytical Geomicrobiology. - : Cambridge University Press. - 9781107707399 - 9781107070332 ; , s. 288-313
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Book chapter (peer-reviewed)abstract
- Fourier-transform infrared (FTIR) spectroscopy is a technique that measures the molecular-level vibrations in a material, such as a bacterial biofilm, to get a better understanding of the chemistry of the system. This technique is best used to observe changes in a system, e.g., how bacteria protonate and deprotonate as a function of pH or how contaminants sorb to minerals/bacteria, or for tracking the precipitation of a mineral or the breakdown of a contaminant in a system. It can also be used to identify the presence of a specific contaminant in a system, e.g., the presence of bacteria on an antimicrobial surface or the presence of pesticides in water. The will outline the different ways in which FTIR spectroscopy may be used to analyze a variety of samples in geomicrobiology. The techniques and their applicability are detailed, from individual sample recording (via diffuse reflectance measurements) to continuous monitoring of systems (using attenuated total reflectance measurements) and spatially resolved microspectroscopic analysis (either as imaging or as determining the positions for point sampling in a heterogeneous sample), and a general strategy for data handling is given, including the basics of some multivariate techniques. We will explain how to get the best possible data using each FTIR spectroscopic method, as well as how to best treat your data before analysis. Additionally, this chapter deals with understanding how to identify the representative FTIR bands for bacteria, and how those bands can change as a function of pH.
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| 8. |
- Lundberg-Felten, Judith, et al.
(author)
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Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen
- 2018
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In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 218:3, s. 999-1014
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Journal article (peer-reviewed)abstract
- The phytohormone ethylene impacts secondary stem growth in plants by stimulating cambial activity, xylem development and fiber over vessel formation. We report the effect of ethylene on secondary cell wall formation and the molecular connection between ethylene signaling and wood formation. We applied exogenous ethylene or its precursor 1-aminocyclopropane-1-carboxylic acid (ACC) to wild-type and ethylene-insensitive hybrid aspen trees (Populus tremulaxtremuloides) and studied secondary cell wall anatomy, chemistry and ultrastructure. We furthermore analyzed the transcriptome (RNA Seq) after ACC application to wild-type and ethylene-insensitive trees. We demonstrate that ACC and ethylene induce gelatinous layers (G-layers) and alter the fiber cell wall cellulose microfibril angle. G-layers are tertiary wall layers rich in cellulose, typically found in tension wood of aspen trees. A vast majority of transcripts affected by ACC are downstream of ethylene perception and include a large number of transcription factors (TFs). Motif-analyses reveal potential connections between ethylene TFs (Ethylene Response Factors (ERFs), ETHYLENE INSENSITIVE 3/ETHYLENE INSENSITIVE3-LIKE1 (EIN3/EIL1)) and wood formation. G-layer formation upon ethylene application suggests that the increase in ethylene biosynthesis observed during tension wood formation is important for its formation. Ethylene-regulated TFs of the ERF and EIN3/EIL1 type could transmit the ethylene signal.
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| 9. |
- Lundberg-Felten, Judith, et al.
(author)
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Vibrational spectroscopic image analysis of biological material using multivariate curve resolution-alternating least squares (MCR-ALS)
- 2015
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In: Nature Protocols. - : Springer Science and Business Media LLC. - 1754-2189 .- 1750-2799. ; 10:2, s. 217-240
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Journal article (peer-reviewed)abstract
- Raman and Fourier transform IR (FTIR) microspectroscopic images of biological material (tissue sections) contain detailed information about their chemical composition. The challenge lies in identifying changes in chemical composition, as well as locating and assigning these changes to different conditions (pathology, anatomy, environmental or genetic factors). Multivariate data analysis techniques are ideal for decrypting such information from the data. This protocol provides a user-friendly pipeline and graphical user interface (GUI) for data pre-processing and unmixing of pixel spectra into their contributing pure components by multivariate curve resolution-alternating least squares (MCR-ALS) analysis. The analysis considers the full spectral profile in order to identify the chemical compounds and to visualize their distribution across the sample to categorize chemically distinct areas. Results are rapidly achieved (usually <30-60 min per image), and they are easy to interpret and evaluate both in terms of chemistry and biology, making the method generally more powerful than principal component analysis (PCA) or heat maps of single-band intensities. In addition, chemical and biological evaluation of the results by means of reference matching and segmentation maps (based on k-means clustering) is possible.
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| 10. |
- Nord, Christoffer, et al.
(author)
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Biochemical profiling of diabetes disease progression by multivariate vibrational microspectroscopy of the pancreas
- 2017
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In: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7:1, s. 6646-
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Journal article (peer-reviewed)abstract
- Despite the dramatic increase in the prevalence of diabetes, techniques for in situ studies of the underlying pancreatic biochemistry are lacking. Such methods would facilitate obtaining mechanistic understanding of diabetes pathophysiology and aid in prognostic and/or diagnostic assessments. In this report we demonstrate how a multivariate imaging approach (orthogonal projections to latent structures - discriminant analysis) can be applied to generate full vibrational microspectroscopic profiles of pancreatic tissues. These profiles enable extraction of known and previously unrecorded biochemical alterations in models of diabetes, and allow for classification of the investigated tissue with regards to tissue type, strain and stage of disease progression. Most significantly, the approach provided evidence for dramatic alterations of the pancreatic biochemistry at the initial onset of immune-infiltration in the Non Obese Diabetic model for type 1 diabetes. Further, it enabled detection of a previously undocumented accumulation of collagen fibrils in the leptin deficient ob/ob mouse islets. By generating high quality spectral profiles through the tissue capsule of hydrated human pancreata and by in vivo Raman imaging of pancreatic islets transplanted to the anterior chamber of the eye, we provide critical feasibility studies for the translation of this technique to diagnostic assessments of pancreatic biochemistry in vivo.
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